
@Article{Detjen:855672,
  Author          = {Detjen, Katharina M. and Otto, Raik and Giesecke, Yvonne
                    and Geisler, Lukas and Riemer, Pamela and Jann, Henning
                    and Grötzinger, Carsten and Sers, Christine and Pascher,
                    Andreas and Lüdde, Tom and Leser, Ulf and Wiedenmann,
                    Bertram and Sigal, Michael and Tacke, Frank and
                    Roderburg, Christoph and Hammerich, Linda},
  Title           = {Elevated {Flt3L} Predicts Long-Term Survival in Patients
                    with High-Grade Gastroenteropancreatic Neuroendocrine
                    Neoplasms},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2021},
  DOI             = {10.3390/cancers13174463},
  Number          = {17},
  Pages           = {4463},
  Volume          = {13}
}

@Article{Kather:855673,
  Author          = {Kather, Jakob Nikolas and Heij, Lara R. and Grabsch,
                    Heike I. and Loeffler, Chiara and Echle, Amelie and Muti,
                    Hannah Sophie and Krause, Jeremias and Niehues, Jan M.
                    and Sommer, Kai A. J. and Bankhead, Peter and Kooreman,
                    Loes F. S. and Schulte, Jefree J. and Cipriani, Nicole A.
                    and Buelow, Roman D. and Boor, Peter and Ortiz-Brüchle,
                    Nadina and Hanby, Andrew M. and Speirs, Valerie and
                    Kochanny, Sara and Patnaik, Akash and Srisuwananukorn,
                    Andrew and Brenner, Hermann and Hoffmeister, Michael and
                    van den Brandt, Piet A. and Jäger, Dirk and Trautwein,
                    Christian and Pearson, Alexander T. and Luedde, Tom},
  Title           = {Pan-cancer image-based detection of clinically
                    actionable genetic alterations},
  JournalTitle    = {Nature Cancer},
  Date            = {2020},
  DOI             = {10.1038/s43018-020-0087-6},
  Number          = {8},
  Pages           = {789--799},
  Volume          = {1}
}

@Article{Labiano:855675,
  Author          = {Labiano, Ibone and Agirre-Lizaso, Aloña and Olaizola,
                    Paula and Echebarria, Anne and Huici-Izagirre, Maider and
                    Olaizola, Irene and Esparza-Baquer, Aitor and Sharif,
                    Omar and Hijona, Elizabeth and Milkiewicz, Piotr and
                    Milkiewicz, Malgorzata and González-Romero, Francisco
                    and Aspichueta, Patricia and Monte, Maria J. and Marin,
                    Jose J.G. and Vucur, Mihael and Luedde, Tom and Marzioni,
                    Marco and Mann, Derek A. and Bujanda, Luis and Rodrigues,
                    Pedro M. and Banales, Jesus M. and Perugorria, Maria J.},
  Title           = {{TREM}-2 plays a protective role in cholestasis by
                    acting as a negative regulator of inflammation},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2022.05.044},
  Number          = {4},
  Pages           = {991--1004},
  Volume          = {77}
}

@Article{Ghallab:855677,
  Author          = {Ghallab, Ahmed and Hassan, Reham and Hofmann, Ute and
                    Friebel, Adrian and Hobloss, Zaynab and Brackhagen, Lisa
                    and Begher-Tibbe, Brigitte and Myllys, Maiju and
                    Reinders, Joerg and Overbeck, Nina and Sezgin, Selahaddin
                    and Zühlke, Sebastian and Seddek, Abdel-latif and Murad,
                    Walaa and Brecklinghaus, Tim and Kappenberg, Franziska
                    and Rahnenführer, Jörg and González, Daniela and
                    Goldring, Christopher and Copple, Ian M. and Marchan,
                    Rosemarie and Longerich, Thomas and Vucur, Mihael and
                    Luedde, Tom and Urban, Stephan and Canbay, Ali and
                    Schreiter, Thomas and Trauner, Michael and Akakpo, Jephte
                    Y. and Olyaee, Mojtaba and Curry, Steven C. and Sowa,
                    Jan-Peter and Jaeschke, Hartmut and Hoehme, Stefan and
                    Hengstler, Jan G.},
  Title           = {Interruption of bile acid uptake by hepatocytes after
                    acetaminophen overdose ameliorates hepatotoxicity},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2022.01.020},
  Number          = {1},
  Pages           = {71--83},
  Volume          = {77}
}

@Article{Müller:846176,
  Author          = {Müller, Katrin and Honcharova-Biletska, Hanna and
                    Koppe, Christiane and Egger, Michèle and Chan, Lap Kwan
                    and Schneider, Anne T. and Küsgens, Lena and Böhm,
                    Friederike and Boege, Yannick and Healy, Marc E. and
                    Schmitt, Johannes and Comtesse, Sarah and Castoldi, Mirco
                    and Preisinger, Christian and Szydlowska, Marta and
                    Focaccia, Enrico and Gaisa, Nadine T. and Loosen, Sven H.
                    and Jörs, Simone and Tacke, Frank and Roderburg,
                    Christoph and Keitel, Verena and Bode, Johannes G. and
                    Boor, Peter and Davis, Roger J. and Longerich, Thomas and
                    Geisler, Fabian and Heikenwalder, Mathias and Weber,
                    Achim and Vucur, Mihael and Luedde, Tom},
  Title           = {{JNK} signaling prevents biliary cyst formation through
                    a {CASPASE}-8–dependent function of {RIPK1} during
                    aging},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2021},
  DOI             = {10.1073/pnas.2007194118},
  Number          = {12},
  Pages           = {e2007194118},
  Volume          = {118}
}

@Article{SchulzeHagen:851422,
  Author          = {Schulze-Hagen, Maximilian F. and Roderburg, Christoph
                    and Wirtz, Theresa H. and Jördens, Markus S. and
                    Bündgens, Lukas and Abu Jhaisha, Samira and Hohlstein,
                    Philipp and Brozat, Jonathan F. and Bruners, Philipp and
                    Loberg, Christina and Kuhl, Christiane and Trautwein,
                    Christian and Tacke, Frank and Luedde, Tom and Loosen,
                    Sven H. and Koch, Alexander},
  Title           = {Decreased Bone Mineral Density Is a Predictor of Poor
                    Survival in Critically Ill Patients},
  JournalTitle    = {J. Clin. Med.},
  Date            = {2021},
  DOI             = {10.3390/jcm10163741},
  Number          = {16},
  Pages           = {3741},
  Volume          = {10}
}

@Article{Echle:813402,
  Author          = {Echle, Amelie and Grabsch, Heike Irmgard and Quirke,
                    Philip and van den Brandt, Piet A. and West, Nicholas P.
                    and Hutchins, Gordon G.A. and Heij, Lara R. and Tan,
                    Xiuxiang and Richman, Susan D. and Krause, Jeremias and
                    Alwers, Elizabeth and Jenniskens, Josien and Offermans,
                    Kelly and Gray, Richard and Brenner, Hermann and
                    Chang-Claude, Jenny and Trautwein, Christian and Pearson,
                    Alexander T. and Boor, Peter and Luedde, Tom and Gaisa,
                    Nadine Therese and Hoffmeister, Michael and Kather, Jakob
                    Nikolas},
  Title           = {Clinical-Grade Detection of Microsatellite Instability
                    in Colorectal Tumors by Deep Learning},
  JournalTitle    = {Gastroenterology},
  Date            = {2020},
  DOI             = {10.1053/j.gastro.2020.06.021},
  Number          = {4},
  Pages           = {1406--1416.e11},
  Volume          = {159}
}

@Article{Roderburg:846384,
  Author          = {Roderburg, Christoph and Loosen, Sven H. and Bednarsch,
                    Jan and Alizai, Patrick H. and Roeth, Anjali A. and
                    Schmitz, Sophia M. and Vucur, Mihael and Luedde, Mark and
                    Paffenholz, Pia and Tacke, Frank and Trautwein, Christian
                    and Ulmer, Tom F. and Neumann, Ulf Peter and Luedde,
                    Tom},
  Title           = {Levels of Circulating {PD}-L1 Are Decreased in Patients
                    with Resectable Cholangiocarcinoma},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2021},
  DOI             = {10.3390/ijms22126569},
  Number          = {12},
  Pages           = {6569},
  Volume          = {22}
}

@Article{AbouElkacem:233745,
  Author          = {Abou-Elkacem, Lotfi and Arns, Susanne and Brix, Gunnar
                    and Gremse, Felix and Zopf, Dieter and Kiessling, Fabian
                    and Lederle, Wiltrud},
  Title           = {Regorafenib Inhibits Growth, Angiogenesis, and
                    Metastasis in a Highly Aggressive, Orthotopic Colon
                    Cancer Model},
  JournalTitle    = {Mol. Cancer Ther.},
  Date            = {2013},
  DOI             = {10.1158/1535-7163.mct-12-1162},
  Keywords        = {Lederle-Selection},
  Number          = {7},
  Pages           = {1322--1331},
  ShortJournal    = {MCT},
  Volume          = {12}
}

@Article{Afrizal2022-us,
  Author          = {Afrizal, Afrizal and Hitch, Thomas C. A. and Viehof,
                    Alina and Treichel, Nicole and Riedel, Thomas and Abt,
                    Birte and Buhl, Eva M. and Kohlheyer, Dietrich and
                    Overmann, Jörg and Clavel, Thomas},
  Title           = {Anaerobic single‐cell dispensing facilitates the
                    cultivation of human gut bacteria},
  JournalTitle    = {Method. Enzymol.},
  Date            = {2022},
  Options         = {openaccess=auto},
  doi+an:default  = {=openaccess},
  DOI             = {10.1111/1462-2920.15935},
  Keywords        = {Clavel-Selection},
  Number          = {9},
  Pages           = {3861--3881},
  Volume          = {24}
}

@Article{Afrizal:854345,
  Author          = {Afrizal, Afrizal and Jennings, Susan A. V. and Hitch,
                    Thomas C. A. and Riedel, Thomas and Basic, Marijana and
                    Panyot, Atscharah and Treichel, Nicole and Hager, Fabian
                    T. and Wong, Erin Oi-Yan and Wolter, Birger and Viehof,
                    Alina and von Strempel, Alexandra and Eberl, Claudia and
                    Buhl, Eva M. and Abt, Birte and Bleich, André and Tolba,
                    René and Blank, Lars Mathias and Navarre, William W. and
                    Kießling, Fabian and Horz, Hans-Peter and Torow, Natalia
                    and Cerovic, Vuk and Stecher, Bärbel and Strowig, Till
                    and Overmann, Jörg and Clavel, Thomas},
  Title           = {Enhanced cultured diversity of the mouse gut microbiota
                    enables custom-made synthetic communities},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2022},
  Keywords        = {Clavel-Selection},
  DOI             = {10.1016/j.chom.2022.09.011},
  Pages           = {S193131282200467X},
  Volume          = {30}
}

@Article{Aggarwal2020-ky,
  Author          = {Aggarwal, Nikhil and Breedon, Amy M Ehrenworth and
                    Davis, Christina M and Hwang, In Young and Chang, Matthew
                    Wook},
  Title           = {Engineering probiotics for therapeutic applications:
                    recent examples and translational outlook},
  JournalTitle    = {Curr. Opin. Biotechnol.},
  Date            = {2020},
  DOI             = {10.1016/j.copbio.2020.02.016},
  Pages           = {171--179},
  Volume          = {65}
}

@Book{Aizawa2014flagellar,
  Author          = {Aizawa, Shin-Ichi},
  Title           = {The flagellar world: {Electron} microscopic images of
                    bacterial flagella and related surface structures from
                    more than 30 species},
  Date            = {2014},
  ISBN            = {978-0-12-417234-0}
}

@Article{Akahoshi2022Flagella,
  Author          = {Akahoshi, Douglas T. and Bevins, Charles L.},
  Title           = {Flagella at the Host-Microbe Interface: {Key} Functions
                    Intersect With Redundant Responses},
  JournalTitle    = {Front. Immunol.},
  Date            = {2022-03-24},
  DOI             = {10.3389/fimmu.2022.828758},
  Pages           = {828758},
  Volume          = {13}
}

@Article{Akiba2020-zj,
  Author          = {Akiba, Yasutada and Maruta, Koji and Takajo, Takeshi and
                    Narimatsu, Kazuyuki and Said, Hyder and Kato, Ikuo and
                    Kuwahara, Atsukazu and Kaunitz, Jonathan D.},
  Title           = {Lipopolysaccharides transport during fat absorption in
                    rodent small intestine},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2020},
  DOI             = {10.1152/ajpgi.00079.2020},
  Number          = {6},
  Pages           = {G1070--G1087},
  Volume          = {318}
}

@Article{AlRawashdeh:238895,
  Author          = {Al Rawashdeh, Wa'el and Arns, Susanne and Gremse, Felix
                    and Ehling, Josef and Knüchel-Clarke, Ruth and Kray,
                    Stefan and Spöler, Felix and Kiessling, Fabian and
                    Lederle, Wiltrud},
  Title           = {Optical Tomography of {MMP} Activity Allows a Sensitive
                    Noninvasive Characterization of the Invasiveness and
                    Angiogenesis of {SCC} Xenografts},
  JournalTitle    = {Neoplasia},
  Date            = {2014},
  DOI             = {10.1016/j.neo.2014.03.005},
  Number          = {3},
  Pages           = {235--246.e1},
  Volume          = {16}
}

@Article{AlRawashdeh:689556,
  Author          = {Rawashdeh, Wa'el Al and Zuo, Simin and Melle, Andrea and
                    Appold, Lia and Koletnik, Susanne and Tsvetkova, Yoanna
                    and Beztsinna, Nataliia and Pich, Andrij and Lammers,
                    Twan and Kiessling, Fabian and Gremse, Felix},
  Title           = {Noninvasive Assessment of Elimination and Retention
                    using {CT}-{FMT} and Kinetic Whole-body Modeling},
  JournalTitle    = {Theranostics},
  Date            = {2017},
  DOI             = {10.7150/thno.17263},
  Keywords        = {Gremse-Selection},
  Number          = {6},
  Pages           = {1499--1510},
  Volume          = {7}
}

@Article{Awoniyi2022-gp,
  Author          = {Awoniyi, Muyiwa and Wang, Jeremy and Ngo, Billy and
                    Meadows, Vik and Tam, Jason and Viswanathan, Amba and
                    Lai, Yunjia and Montgomery, Stephanie and Farmer, Morgan
                    and Kummen, Martin and Thingholm, Louise and Schramm,
                    Christoph and Bang, Corinna and Franke, Andre and Lu, Kun
                    and Zhou, Huiping and Bajaj, Jasmohan S and Hylemon,
                    Phillip B and Ting, Jenny and Popov, Yury V and Hov,
                    Johannes Roksund and Francis, Heather L and Sartor, Ryan
                    Balfour},
  Title           = {Protective and aggressive bacterial subsets and
                    metabolites modify hepatobiliary inflammation and
                    fibrosis in a murine model of {PSC}},
  JournalTitle    = {Gut},
  Date            = {2022},
  DOI             = {10.1136/gutjnl-2021-326500},
  Pages           = {gutjnl--2021--326500}
}

@Article{Albillos2020gut-liver,
  Author          = {Albillos, Agustín and de Gottardi, Andrea and Rescigno,
                    María},
  Title           = {The gut-liver axis in liver disease:
                    {Pathophysiological} basis for therapy},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020-03},
  DOI             = {10.1016/j.jhep.2019.10.003},
  Number          = {3},
  Pages           = {558--577},
  Volume          = {72}
}

@Article{Allen2010-nx,
  Author          = {Allen, Irving C. and TeKippe, Erin McElvania and
                    Woodford, Rita-Marie T. and Uronis, Joshua M. and Holl,
                    Eda K. and Rogers, Arlin B. and Herfarth, Hans H. and
                    Jobin, Christian and Ting, Jenny P.-Y.},
  Title           = {The {NLRP3} inflammasome functions as a negative
                    regulator of tumorigenesis during colitis-associated
                    cancer},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2010},
  DOI             = {10.1084/jem.20100050},
  Number          = {5},
  Pages           = {1045--1056},
  Volume          = {207}
}

@Article{Almeida2022-bo,
  Author          = {Almeida, Joana I. and Tenreiro, Miguel F. and
                    Martinez-Santamaria, Lucía and Guerrero-Aspizua, Sara
                    and Gisbert, Javier P. and Alves, Paula M. and Serra,
                    Margarida and Baptista, Pedro M.},
  Title           = {Hallmarks of the human intestinal microbiome on liver
                    maturation and function},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2021.10.015},
  Keywords        = {Liver development; hepatic maturation and function;
                    human intestinal microbiome; microbial metabolites;
                    microbiota},
  Number          = {3},
  Pages           = {694--725},
  Volume          = {76}
}

@Article{Anadol2014,
  Author          = {Anadol, Evrim and Schierwagen, Robert and Elfimova,
                    Natalia and Tack, Katharina and Schwarze-Zander,
                    Carolynne and Eischeid, Hanna and Noetel, Andrea and
                    Boesecke, Christoph and Jansen, Christian and Dold, Leona
                    and Wasmuth, Jan-Christian and Strassburg, Christian P.
                    and Spengler, Ulrich and Rockstroh, Jürgen Kurt and
                    Odenthal, Margarete and Trebicka, Jonel},
  Title           = {Circulating {MicroRNAs} as a marker for liver injury in
                    human immunodeficiency virus patients},
  JournalTitle    = {Hepatology},
  Date            = {2014},
  DOI             = {10.1002/hep.27369},
  Number          = {1},
  Pages           = {46--55},
  Volume          = {61}
}

@Article{Arab2018,
  Author          = {Arab, J. P. and Martin-Mateos, R. M. and Shah, V. H.},
  Title           = {Gut-liver axis, cirrhosis and portal hypertension: {The}
                    chicken and the egg},
  JournalTitle    = {Hepatol. Int.},
  Date            = {2018},
  DOI             = {10.1007/s12072-017-9798-x},
  Note            = {NIHMS1059573},
  Number          = {Suppl 1},
  Pages           = {24--33},
  Volume          = {12}
}

@Article{Armitage1997Bacterial,
  Author          = {Armitage, Judith P. and Schmitt, Rudiger},
  Title           = {Bacterial chemotaxis: {Rhodobacter} sphaeroide and
                    Sinorhizobium meliloti - variations on a theme?},
  JournalTitle    = {Microbiology},
  Date            = {1997},
  DOI             = {10.1099/00221287-143-12-3671},
  Number          = {12},
  Pages           = {3671--3682},
  Volume          = {143}
}

@Article{Arts:716555,
  Author          = {Arts, Martijn and Soons, Zita and Ellis, Shane R. and
                    Pierzchalski, Keely A. and Balluff, Benjamin and Eijkel,
                    Gert B. and Dubois, Ludwig J. and Lieuwes, Natasja G. and
                    Agten, Stijn M. and Hackeng, Tilman M. and van Loon, Luc
                    J. C. and Heeren, Ron M. A. and Olde Damink, Steven W.
                    M.},
  Title           = {Detection of Localized Hepatocellular Amino Acid
                    Kinetics by using Mass Spectrometry Imaging of Stable
                    Isotopes},
  JournalTitle    = {Angew. Chem. Int. Ed.},
  Date            = {2017},
  DOI             = {10.1002/anie.201702669},
  Keywords        = {Olde Damink-Selection},
  Number          = {25},
  Pages           = {7146--7150},
  Volume          = {56}
}

@Article{Asare:238234,
  Author          = {Asare, Yaw and Shagdarsuren, Erdenechimeg and Schmid,
                    Johannes and Tilstam, Pathricia and Grommes, Jochen and
                    El Bounkari, Omar and Schütz, Anke and Weber, Christian
                    and de Winther, Menno and Noels, Heidi and Bernhagen,
                    Jürgen},
  Title           = {Endothelial {CSN5} impairs {NF}-{κB} activation and
                    monocyte adhesion to endothelial cells and is highly
                    expressed in human atherosclerotic lesions},
  JournalTitle    = {Thromb. Haemostasis},
  Date            = {2013},
  DOI             = {10.1160/th13-02-0155},
  Number          = {07},
  Pages           = {141--152},
  Volume          = {110}
}

@Article{Asare:721877,
  Author          = {Asare, Yaw and Ommer, Miriam and Azombo, Florence. A.
                    and Alampour-Rajabi, Setareh and Sternkopf, Marieke and
                    Sanati, Maryam and Gijbels, Marion J. and Schmitz,
                    Corinna and Sinitski, Dzmitry and Tilstam, Pathricia V.
                    and Lue, Hongqi and Gessner, André and Lange, Denise and
                    Schmid, Johannes A. and Weber, Christian and Dichgans,
                    Martin and Jankowski, Joachim and Pardi, Ruggero and de
                    Winther, Menno P. J. and Noels, Heidi and Bernhagen,
                    Jürgen},
  Title           = {Inhibition of atherogenesis by the {COP9} signalosome
                    subunit 5 in vivo},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2017},
  Addendum        = sharedlast,
  author+an:default = {20=sharedLast;21=sharedLast},
  DOI             = {10.1073/pnas.1618411114},
  Number          = {13},
  Pages           = {E2766--E2775},
  Volume          = {114}
}

@Article{Wallace2022-zk,
  Author          = {Wallace, Sebastian J. and Tacke, Frank and Schwabe,
                    Robert F. and Henderson, Neil C.},
  Title           = {Understanding the cellular interactome of non-alcoholic
                    fatty liver disease},
  JournalTitle    = {JHEP Reports},
  Date            = {2022},
  DOI             = {10.1016/j.jhepr.2022.100524},
  Number          = {8},
  Pages           = {100524},
  Volume          = {4}
}

@Article{Braadland2022,
  Author          = {Braadland, Peder Rustøen and Schneider, Kai Markus and
                    Bergquist, Annika and Molinaro, Antonio and
                    Lövgren-Sandblom, Anita and Henricsson, Marcus and
                    Karlsen, Tom Hemming and Vesterhus, Mette and Trautwein,
                    Christian and Hov, Johannes Roksund and Marschall,
                    Hanns-Ulrich},
  DOI             = {10.1016/j.jhepr.2022.100561},
  Year            = {2022},
  author+an       = {1=equal;2=equal},
  Addendum        = equal,
  Volume          = {4},
  Number          = {11},
  Pages           = {100561},
  Title           = {Suppression of bile acid synthesis as a tipping point in
                    the disease course of primary sclerosing cholangitis},
  JournalTitle    = {JHEP Reports}
}

@Article{Athinarayanan2021-dn,
  Author          = {Athinarayanan, Shaminie and Fan, Yang-Yi and Wang,
                    Xiaokun and Callaway, Evelyn and Cai, Defeng and
                    Chalasani, Naga and Chapkin, Robert S and Liu, Wanqing},
  Title           = {Fatty acid desaturase 1 influences hepatic lipid
                    homeostasis by modulating the {PPAR$\alpha$-FGF21} axis},
  JournalTitle    = {Hepatology Communications},
  Date            = {2021},
  DOI             = {10.1002/hep4.1629},
  Number          = {3},
  Pages           = {461--477},
  Volume          = {5}
}

@Article{Ay:842081,
  Author          = {Ay, Ümran and Lenicek, Martin and Classen, Arno and
                    Olde Damink, Steven W. M. and Bolm, Carsten and Schaap,
                    Frank G.},
  Title           = {New Kids on the Block},
  JournalTitle    = {Metabolites},
  Date            = {2022},
  DOI             = {10.3390/metabo12020176},
  Keywords        = {,CRC1382-Project A07,CRC1382-Project A07,CRC1382-Project
                    A07},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {176},
  Subtitle        = {Bile Salt Conjugates of Microbial Origin},
  Volume          = {12}
}

@Article{Baaten2021-ev,
  Author          = {Baaten, Constance C.F.M.J. and Sternkopf, Marieke and
                    Henning, Tobias and Marx, Nikolaus and Jankowski, Joachim
                    and Noels, Heidi},
  Title           = {Platelet Function in {CKD:} {A} Systematic Review and
                    Meta-Analysis},
  JournalTitle    = {J. Am. Soc. Nephrol.},
  Date            = {2021},
  DOI             = {10.1681/asn.2020101440},
  Keywords        = {Noels-Selection},
  Number          = {7},
  Pages           = {1583--1598},
  Volume          = {32}
}

@Article{Babbar:782496,
  Author          = {Babbar, Anshu and Hitch, Thomas C. A. and Pabst, Oliver
                    and Clavel, Thomas and Hübel, Jessica and Eswaran,
                    Sreepradha and Wagner, Norbert and Schippers, Angela},
  Title           = {The Compromised Mucosal Immune System of β7
                    Integrin-Deficient Mice Has Only Minor Effects on the
                    Fecal Microbiota in Homeostasis},
  JournalTitle    = {Front. Microbiol.},
  Date            = {2019},
  DOI             = {10.3389/fmicb.2019.02284},
  Keywords        = {,CRC1382-Project A05,CRC1382-Project Q02,CRC1382-Project
                    B02,CRC1382-Project B06,CRC1382-Project
                    Q04,CRC1382-Project B02,CRC1382-Project B02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {2284},
  Volume          = {10}
}

@Article{Baeck:132897,
  Author          = {Baeck, Christer and Wehr, Alexander and Karlmark, Karlin
                    Raja and Heymann, Felix and Vucur, Mihael and Gassler,
                    Nikolaus and Huss, Sebastian and Klussmann, Sven and
                    Eulberg, Dirk and Luedde, Tom and Trautwein, Christian
                    and Tacke, Frank},
  Title           = {Pharmacological inhibition of the chemokine {CCL2}
                    {(MCP}-1) diminishes liver macrophage infiltration and
                    steatohepatitis in chronic hepatic injury},
  JournalTitle    = {Gut},
  Date            = {2011},
  DOI             = {10.1136/gutjnl-2011-300304},
  Keywords        = {Tacke-Selection},
  Number          = {3},
  Pages           = {416--426},
  Volume          = {61}
}

@Article{Baetke:685226,
  Author          = {Baetke, Sarah C. and Rix, Anne and Tranquart, François
                    and Schneider, Richard and Lammers, Twan and Kiessling,
                    Fabian and Lederle, Wiltrud},
  Title           = {Squamous Cell Carcinoma Xenografts: {Use} of
                    {VEGFR2}-targeted Microbubbles for Combined Functional
                    and Molecular {US} to Monitor Antiangiogenic Therapy
                    Effects},
  JournalTitle    = {Radiology},
  Date            = {2016},
  DOI             = {10.1148/radiol.2015142899},
  Keywords        = {Lederle-Selection},
  Number          = {2},
  Pages           = {430--440},
  Volume          = {278}
}

@Article{Baier:828360,
  Author          = {Baier, Vanessa and Clayton, Olivia and Nudischer, Ramona
                    and Cordes, Henrik and Schneider, Annika R. P. and Thiel,
                    Christoph Werner Josef and Wittenberger, Timo and Moritz,
                    Wolfgang and Blank, Lars Mathias and Neumann, Ulf Peter
                    and Trautwein, Christian and Kelm, Jens and Schrooders,
                    Yannick and Caiment, Florian and Gmuender, Hans and Roth,
                    Adrian and Castell, José V. and Kleinjans, Jos and
                    Kuepfer, Lars},
  Title           = {A Model-Based Workflow to Benchmark the Clinical
                    Cholestasis Risk of Drugs},
  JournalTitle    = {Clin. Pharmacol. Ther.},
  Date            = {2021},
  DOI             = {10.1002/cpt.2406},
  doi+an:default  = {=openaccess},
  ids             = {Baier2021-im},
  Keywords        = {Küpfer-Selection,CRC1382-Project A06,CRC1382-Project
                    A06,CRC1382-Project A06,CRC1382-Project
                    A01,CRC1382-Project A06,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {5},
  Pages           = {1293--1301},
  ShortJournal    = {CPT},
  Volume          = {110}
}

@Article{Bajaj2021Multiple,
  Author          = {Bajaj, Jasmohan S and Shamsaddini, Amirhossein and
                    Acharya, Chathur and Fagan, Andrew and Sikaroodi,
                    Masoumeh and Gavis, Edith and McGeorge, Sara and Khoruts,
                    Alexander and Fuchs, Michael and Sterling, Richard K and
                    Lee, Hannah and Gillevet, Patrick M},
  Title           = {Multiple bacterial virulence factors focused on
                    adherence and biofilm formation associate with outcomes
                    in cirrhosis},
  JournalTitle    = {Gut Microbes},
  Date            = {2021-01-01},
  DOI             = {10.1080/19490976.2021.1993584},
  Number          = {1},
  Pages           = {1993584},
  Volume          = {13}
}

@Article{Brozat:844848,
  Author          = {Brozat, Jonathan F. and Brandt, Elisa Fabiana and Stark,
                    Myriam and Fischer, Petra and Wirtz, Theresa and
                    Flaßhove, Alexander and Rodenhausen, Aaron N. and Vajen,
                    Tanja and Heinzmann, Alexandra C. A. and Schmitz, Sophia
                    Marie-Therese and Abu Jhaisha, Samira and Röth, Anjali
                    Anna Joy and Koenen, Rory R. and Sahin, Hacer and
                    Trautwein, Christian and Berres, Marie-Luise},
  Title           = {{JAM}–A is a multifaceted regulator in hepatic
                    fibrogenesis, supporting {LSEC} integrity and stellate
                    cell quiescence},
  JournalTitle    = {Liver Int.},
  Date            = {2022},
  DOI             = {10.1111/liv.15187},
  Keywords        = {,CRC1382-Project B04,CRC1382-Project B04,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {5},
  Pages           = {1185--1203},
  Volume          = {42}
}

@Article{Bakker2022-bc,
  Author          = {Bakker, Brenda and Vaes, Rianne D. W. and Aberle, Merel
                    R. and Welbers, Tessa and Hankemeier, Thomas and Rensen,
                    Sander S. and Olde Damink, Steven W. M. and Heeren, Ron
                    M. A.},
  Title           = {Preparing ductal epithelial organoids for
                    high-spatial-resolution molecular profiling using mass
                    spectrometry imaging},
  JournalTitle    = {Nat. Protoc.},
  Date            = {2022},
  DOI             = {10.1038/s41596-021-00661-8},
  Keywords        = {Olde Damink-Selection},
  Number          = {4},
  Pages           = {962--979},
  Volume          = {17}
}

@Article{Bangen2017,
  Author          = {Bangen, Jörg-Martin and Hammerich, Linda and Sonntag,
                    Roland and Baues, Maike and Haas, Ute and Lambertz,
                    Daniela and Longerich, Thomas and Lammers, Twan and
                    Tacke, Frank and Trautwein, Christian and Liedtke,
                    Christian},
  Title           = {Targeting {CCl4} -induced liver fibrosis by {RNA}
                    interference-mediated inhibition of cyclin E1 in mice},
  JournalTitle    = {Hepatology},
  Date            = {2017},
  DOI             = {10.1002/hep.29275},
  Keywords        = {Liedtke-Selection},
  Number          = {4},
  Pages           = {1242--1257},
  Volume          = {66}
}

@Article{Antoniotti2022-gr,
  Author          = {Antoniotti, Carlotta and Rossini, Daniele and
                    Pietrantonio, Filippo and Catteau, Aurélie and
                    Salvatore, Lisa and Lonardi, Sara and Boquet, Isabelle
                    and Tamberi, Stefano and Marmorino, Federica and Moretto,
                    Roberto and Ambrosini, Margherita and Tamburini, Emiliano
                    and Tortora, Giampaolo and Passardi, Alessandro and
                    Bergamo, Francesca and Kassambara, Alboukadel and
                    Sbarrato, Thomas and Morano, Federica and Ritorto,
                    Giuliana and Borelli, Beatrice and Boccaccino, Alessandra
                    and Conca, Veronica and Giordano, Mirella and Ugolini,
                    Clara and Fieschi, Jacques and Papadopulos, Alexia and
                    Massoué, Clémentine and Aprile, Giuseppe and Antonuzzo,
                    Lorenzo and Gelsomino, Fabio and Martinelli, Erika and
                    Pella, Nicoletta and Masi, Gianluca and Fontanini,
                    Gabriella and Boni, Luca and Galon, Jérôme and
                    Cremolini, Chiara},
  Title           = {Upfront {FOLFOXIRI} plus bevacizumab with or without
                    atezolizumab in the treatment of patients with metastatic
                    colorectal cancer {(AtezoTRIBE):} {A} multicentre,
                    open-label, randomised, controlled, phase 2 trial},
  JournalTitle    = {Lancet Oncol},
  Date            = {2022},
  DOI             = {10.1016/s1470-2045(22)00274-1},
  Number          = {7},
  Pages           = {876--887},
  Volume          = {23}
}

@InCollection{Carlessi2019-zt,
  Author          = {Carlessi, Rodrigo and {School of Pharmacy and Biomedical
                    Sciences, Curtin Health Innovation Research Institute,
                    Bentley, WA, Australia} and Köhn-Gaone, Julia and
                    Olynyk, John K and Tirnitz-Parker, Janina E E and {School
                    of Pharmacy and Biomedical Sciences, Curtin Health
                    Innovation Research Institute, Bentley, WA, Australia}
                    and {Fiona Stanley and Fremantle Hospitals, Fremantle and
                    Murdoch, WA, Australia} and {School of Health and Medical
                    Sciences, Edith Cowan University, Joondalup, WA,
                    Australia} and {School of Pharmacy and Biomedical
                    Sciences, Curtin Health Innovation Research Institute,
                    Bentley, WA, Australia} and {Centre for Cell Therapy and
                    Regenerative Medicine, School of Biomedical Sciences, The
                    University of Western Australia, Crawley WA, Australia}},
  Title           = {Mouse models of hepatocellular carcinoma},
  Date            = {2019-10},
  BookTitle       = {Hepatocellular Carcinoma},
  DOI             = {10.15586/hepatocellularcarcinoma.2019.ch4},
  Pages           = {69--94}
}

@Article{Ginhoux2022,
  Author          = {Ginhoux, Florent and Guilliams, Martin and Merad,
                    Miriam},
  Title           = {Expanding dendritic cell nomenclature in the single-cell
                    era},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2022},
  DOI             = {10.1038/s41577-022-00675-7},
  Number          = {2},
  Pages           = {67--68},
  Volume          = {22}
}

@Article{Magen2022,
  Author          = {Magen, Assaf and Hamon, Pauline and Fiaschi, Nathalie
                    and Troncoso, Leanna and Humblin, Etienne and D'souza,
                    Darwin and Dawson, Travis and Park, Matthew D. and Kim,
                    Joel and Hamel, Steven and Buckup, Mark and Chang,
                    Christie and Tabachnikova, Alexandra and Schwartz, Hara
                    and Malissen, Nausicaa and Lavin, Yonit and
                    Soares-Schanoski, Alessandra and Giotti, Bruno and Hegde,
                    Samarth and Mattiuz, Raphaël and Hennequin, Clotilde and
                    Berichel, Jessica Le and Zhao, Zhen and Ward, Stephen and
                    Fiel, Isabel and Price, Colles and Fernandez, Nicolas and
                    He, Jiang and Kou, Baijun and Dobosz, Michael and Li,
                    Lianjie and Adler, Christina and Ni, Min and Wei, Yi and
                    Wang, Wei and Gupta, Namita T. and Kundu, Kunal and
                    Cygan, Kamil and Deering, Raquel P. and Tsankov, Alex and
                    Kim-Schulze, Seunghee and Gnjatic, Sacha and Kenigsberg,
                    Ephraim and Schwartz, Myron and Marron, Thomas U. and
                    Thurston, Gavin and Kamphorst, Alice O. and Merad,
                    Miriam},
  Title           = {Intratumoral {mregDC} and {{CXCL}13} T helper niches
                    enable local differentiation of {{CD}8} T cells following
                    {PD}-1 blockade},
  Date            = {2022},
  DOI             = {10.1101/2022.06.22.497216}
}

@Article{Barabasch:757298,
  Author          = {Barabasch, Alexandra and Heinzel, Alexander and Bruners,
                    Philipp and Kraemer, Nils A. and Kuhl, Christiane K.},
  Title           = {Diffusion-weighted {MRI} Is Superior to {PET/CT} in
                    Predicting Survival of Patients Undergoing {90Y}
                    Radioembolization of Hepatic Metastases},
  JournalTitle    = {Radiology},
  Date            = {2018},
  DOI             = {10.1148/radiol.2018170408},
  Keywords        = {Kuhl-Selection},
  Number          = {3},
  Pages           = {764--773},
  Volume          = {288}
}

@Article{Bartneck:803964,
  Author          = {Bartneck, Matthias and Koppe, Christiane and Fech,
                    Viktor and Warzecha, Klaudia Theresa and Kohlhepp,
                    Marlene and Huss, Sebastian and Weiskirchen, Ralf and
                    Trautwein, Christian and Lüdde, Tom and Tacke, Frank},
  Title           = {Roles of {CCR}2 and {CCR}5 for Hepatic Macrophage
                    Polarization in Mice With Liver Parenchymal Cell-Specific
                    {NEMO} Deletion},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jcmgh.2020.08.012},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project B05,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {327--347},
  ShortJournal    = {CMGH},
  Volume          = {11}
}

@Article{Bagarolo2022,
  Author          = {Bagarolo, Giulia Ilaria and Schierwagen, Robert and Gu,
                    Wenyi and Jankowski, Vera and Soppert, Josefin and
                    Barzakova, Emona and Cascone, Federica and Tyc, Olaf and
                    Kuhl, Christiane and Noels, Heidi and Trebicka, Jonel and
                    Jankowski, Joachim},
  Title           = {Gut-liver crosstalk: Effect of the transjugular
                    intrahepatic portosystemic shunt on peptidomics
                    composition of peripheral plasma},
  JournalTitle    = {RWTH Aachen publication server},
  Date            = {2022},
  DOI             = {10.18154/RWTH-2022-10009}
}

@Article{Becattini2021,
  Author          = {Becattini, Barbara and Breasson, Ludovic and Sardi,
                    Claudia and Zani, Fabio and Solinas, Giovanni},
  Title           = {{PI}3K$\gamma$ promotes obesity-associated
                    hepatocellular carcinoma by regulating metabolism and
                    inflammation},
  JournalTitle    = {JHEP Reports},
  Date            = {2021},
  DOI             = {10.1016/j.jhepr.2021.100359},
  Number          = {6},
  Pages           = {100359},
  Volume          = {3}
}

@Article{Becker2011-oj,
  Author          = {Becker, Natalie and Kunath, Julia and Loh, Gunnar and
                    Blaut, Michael},
  Title           = {Human intestinal microbiota: characterization of a
                    simplified and stable gnotobiotic rat model},
  JournalTitle    = {Gut Microbes},
  Date            = {2011},
  DOI             = {10.4161/gmic.2.1.14651},
  Number          = {1},
  Pages           = {25--33},
  Volume          = {2}
}

@Article{Bednarsch2021-eq,
  Author          = {Bednarsch, Jan and Czigany, Zoltan and Heij, Lara
                    Rosaline and Luedde, Tom and van Dam, Ronald and Lang,
                    Sven Arke and Ulmer, Tom Florian and Hornef, Mathias
                    Walter and Neumann, Ulf Peter},
  Title           = {Bacterial bile duct colonization in perihilar
                    cholangiocarcinoma and its clinical significance},
  JournalTitle    = {Sci. Rep.},
  Addendum        = preliminarywork,
  Date            = {2021},
  DOI             = {10.1038/s41598-021-82378-y},
  ids             = {Bednarsch2021-li},
  Keywords        = {Neumann-Selection},
  Number          = {1},
  Pages           = {2926},
  Volume          = {11}
}

@Article{Bednarsch2021-es,
  Author          = {Bednarsch, Jan and Czigany, Zoltan and Loosen, Sven H
                    and Heij, Lara and Ruckgaber, Lorenz and Maes, Henning
                    and Krause, Jan-Pit and Reen, Matthias and Toteva, Beata
                    and Vosdellen, Theresa and Bruners, Philipp and Lang,
                    Sven Arke and Ulmer, Tom Florian and Roderburg, Christoph
                    and Luedde, Tom and Neumann, Ulf Peter},
  Title           = {Perioperative rifaximin is not associated with enhanced
                    functional and volumetric recovery after major liver
                    resection},
  JournalTitle    = {Sci. Rep.},
  Date            = {2021},
  DOI             = {10.1038/s41598-021-97442-w},
  ids             = {Bednarsch2021-ku},
  Keywords        = {Neumann-Selection},
  Number          = {1},
  Pages           = {17936},
  Volume          = {11}
}

@Article{Bednarsch2022-jm,
  Author          = {Bednarsch, Jan and Tan, Xiuxiang and Czigany, Zoltan and
                    Wiltberger, Georg and Buelow, Roman David and Boor, Peter
                    and Lang, Sven Arke and Ulmer, Tom Florian and Neumann,
                    Ulf Peter and Heij, Lara Rosaline},
  Title           = {Limitations of nerve fiber density as a prognostic
                    marker in predicting oncological outcomes in
                    hepatocellular carcinoma},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2022},
  DOI             = {10.3390/cancers14092237},
  Number          = {9},
  Pages           = {2237},
  Volume          = {14}
}

@Article{Bednarsch:847208,
  Author          = {Bednarsch, Jan and Czigany, Zoltan and Heij, Lara R. and
                    Amygdalos, Iakovos and Heise, Daniel and Bruners, Philip
                    and Ulmer, Tom F. and Neumann, Ulf Peter and Lang, Sven
                    A.},
  Title           = {The role of re-resection in recurrent hepatocellular
                    carcinoma},
  JournalTitle    = {Langenbeck's archives of surgery},
  Date            = {2022},
  DOI             = {10.1007/s00423-022-02545-1},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project A06},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)}
}

@Article{Berlec2015-da,
  Author          = {Berlec, Aleš and Završnik, Janja and Butinar, Miha and
                    Turk, Boris and Štrukelj, Borut},
  Title           = {In vivo imaging of Lactococcus lactis, Lactobacillus
                    plantarum and {Escherichia} coli expressing infrared
                    fluorescent protein in mice},
  JournalTitle    = {Microb. Cell Fact.},
  Date            = {2015},
  DOI             = {10.1186/s12934-015-0376-4},
  Number          = {1},
  Pages           = {181},
  Volume          = {14}
}

@Article{Begley2005-ej,
  Author          = {Begley, Máire and Gahan, Cormac G M and Hill, Colin},
  Title           = {The interaction between bacteria and bile},
  JournalTitle    = {FEMS Microbiol. Rev.},
  Date            = {2005},
  DOI             = {10.1016/j.femsre.2004.09.003},
  Number          = {4},
  Pages           = {625--651},
  Volume          = {29}
}

@Article{Bellais:841321,
  Author          = {Bellais, Samuel and Nehlich, Mélanie and Ania, Maryne
                    and Duquenoy, Aurore and Mazier, Wilfrid and van den
                    Engh, Ger and Baijer, Jan and Treichel, Nicole and
                    Clavel, Thomas and Belotserkovsky, Ilia and Thomas,
                    Vincent},
  Title           = {Species-targeted sorting and cultivation of commensal
                    bacteria from the gut microbiome using flow cytometry
                    under anaerobic conditions},
  JournalTitle    = {Microbiome},
  Date            = {2022},
  DOI             = {10.1186/s40168-021-01206-7},
  Keywords        = {,CRC1382-Project A05,CRC1382-Project Q02,CRC1382-Project
                    Q02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {24},
  Volume          = {10}
}

@Article{Benz:813492,
  Author          = {Benz, Fabian and Bogen, Andreas and Praktiknjo, Michael
                    and Jansen, Christian and Meyer, Carsten and Wree,
                    Alexander and Demir, Muenevver and Loosen, Sven and
                    Vucur, Mihael and Schierwagen, Robert and Tacke, Frank
                    and Trebicka, Jonel and Roderburg, Christoph},
  Title           = {Serum levels of bone sialoprotein correlate with portal
                    pressure in patients with liver cirrhosis},
  JournalTitle    = {PLOS ONE},
  Date            = {2020},
  DOI             = {10.1371/journal.pone.0231701},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project B05,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {e0231701},
  Volume          = {15}
}

@Article{Beraza:166324,
  Author          = {Beraza, Naiara and Malato, Yann and Sander, Leif E. and
                    Al-Masaoudi, Malika and Freimuth, Julia and Riethmacher,
                    Dieter and Gores, Gregory J. and Roskams, Tania and
                    Liedtke, Christian and Trautwein, Christian},
  Title           = {Hepatocyte-specific {NEMO} deletion promotes {NK/NKT}
                    cell– and {TRAIL}-dependent liver damage},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2009},
  DOI             = {10.1084/jem.20082152},
  Keywords        = {Liedtke-Selection},
  Number          = {8},
  Pages           = {1727--1737},
  ShortJournal    = {JEM},
  Volume          = {206}
}

@Article{Berg1972Chemotaxis,
  Author          = {Berg, Howard C. and Brown, Douglas A.},
  Title           = {Chemotaxis in {Escherichia} coli analysed by
                    Three-dimensional Tracking},
  JournalTitle    = {Nature},
  Date            = {1972-10-27},
  DOI             = {10.1038/239500a0},
  Number          = {5374},
  Pages           = {500--504},
  Volume          = {239}
}

@Article{Berntsen2018-tx,
  Author          = {Berntsen, Natalie Lie and Fosby, Bjarte and Valestrand,
                    Laura and Tan, Corey and Reims, Henrik M. and Schrumpf,
                    Elisabeth and Karlsen, Tom Hemming and Line, Pål-Dag and
                    Melum, Espen},
  Title           = {Establishment of a surgical bile duct injection
                    technique giving direct access to the bile ducts for
                    studies of the murine biliary tree},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2018},
  DOI             = {10.1152/ajpgi.00124.2017},
  Number          = {3},
  Pages           = {G349--G359},
  Volume          = {314}
}

@Article{Berres2013-pf,
  Author          = {Berres, Marie-Luise and Allen, Carl E and Merad,
                    Miriam},
  Title           = {Pathological consequence of misguided dendritic cell
                    differentiation in histiocytic diseases},
  JournalTitle    = {Adv. Immunol.},
  Date            = {2013},
  DOI             = {10.1016/B978-0-12-417028-5.00005-3},
  Pages           = {127--161},
  Volume          = {120}
}

@Article{Berres2015,
  Author          = {Berres, Marie-Luise and Lehmann, Jennifer and Jansen,
                    Christian and Görtzen, Jan and Meyer, Carsten and
                    Thomas, Daniel and Zimmermann, Henning W. and Kroy,
                    Daniela and Schumacher, Fabienne and Strassburg,
                    Christian P. and Sauerbruch, Tilman and Trautwein,
                    Christian and Wasmuth, Hermann E. and Trebicka, Jonel},
  Title           = {Chemokine {(C}-X-C motif) ligand 11 levels predict
                    survival in cirrhotic patients with transjugular
                    intrahepatic portosystemic shunt},
  JournalTitle    = {Liver Int.},
  Date            = {2015},
  DOI             = {10.1111/liv.12922},
  Number          = {3},
  Pages           = {386--394},
  Volume          = {36}
}

@Article{Berres:133567,
  Author          = {Berres, Marie-Luise and Papen, Sven and Pauels, Katrin
                    and Schmitz, Petra and Zaldivar, Mirko Moreno and
                    Hellerbrand, Claus and Mueller, Tobias and Berg, Thomas
                    and Weiskirchen, Ralf and Trautwein, Christian and
                    Wasmuth, Hermann E.},
  Title           = {A functional variation in {CHI3L1} is associated with
                    severity of liver fibrosis and {YKL}-40 serum levels in
                    chronic hepatitis C infection},
  JournalTitle    = {J. Hepatol.},
  Date            = {2009},
  DOI             = {10.1016/j.jhep.2008.09.016},
  Number          = {2},
  Pages           = {370--376},
  Volume          = {50}
}

@Article{Berres:175689,
  Author          = {Berres, Marie-Luise and Koenen, Rory R. and Rueland,
                    Anna and Zaldivar, Mirko Moreno and Heinrichs, Daniel and
                    Sahin, Hacer and Schmitz, Petra and Streetz, Konrad L.
                    and Berg, Thomas and Gassler, Nikolaus and Weiskirchen,
                    Ralf and Proudfoot, Amanda and Weber, Christian and
                    Trautwein, Christian and Wasmuth, Hermann E.},
  Title           = {Antagonism of the chemokine Ccl5 ameliorates
                    experimental liver fibrosis in mice},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2010},
  author+an:default = {1=equal;2=equal},
  Addendum        = equal,
  DOI             = {10.1172/jci41732},
  Keywords        = {Berres-Selection},
  Number          = {11},
  Pages           = {4129--4140},
  Volume          = {120}
}

@Article{Berres:194885,
  Author          = {Berres, Marie-Luise and Schlosser, Beate and Berg,
                    Thomas and Trautwein, Christian and Wasmuth, Hermann E.},
  Title           = {Soluble Urokinase Plasminogen Activator Receptor is
                    Associated With Progressive Liver Fibrosis in Hepatitis C
                    Infection},
  JournalTitle    = {J. Clin. Gastroenterol.},
  Date            = {2012},
  DOI             = {10.1097/mcg.0b013e31822da19d},
  Number          = {4},
  Pages           = {334--338},
  Volume          = {46}
}

@Article{Berres:195595,
  Author          = {Berres, Marie-Luise and Trautwein, Christian and
                    Schmeding, Maximilian and Eurich, Dennis and Tacke, Frank
                    and Bahra, Marcus and Neuhaus, Peter and Neumann, Ulf P.
                    and Wasmuth, Hermann E.},
  Title           = {Serum chemokine {CXC} ligand 10 {(CXCL10)} predicts
                    fibrosis progression after liver transplantation for
                    hepatitis C infection},
  JournalTitle    = {Hepatology},
  Date            = {2011},
  DOI             = {10.1002/hep.24098},
  Keywords        = {Berres-Selection,Neumann-Selection},
  Number          = {2},
  Pages           = {596--603},
  Volume          = {53}
}

@Article{Berres:463195,
  Author          = {Berres, Marie-Luise and Lim, Karen Phaik Har and Peters,
                    Tricia and Price, Jeremy and Takizawa, Hitoshi and
                    Salmon, Hélène and Idoyaga, Juliana and Ruzo, Albert
                    and Lupo, Philip J. and Hicks, M. John and Shih, Albert
                    and Simko, Stephen J. and Abhyankar, Harshal and
                    Chakraborty, Rikhia and Leboeuf, Marylene and Beltrão,
                    Monique and Lira, Sérgio A. and Heym, Kenneth M. and
                    Clausen, Björn E. and Bigley, Venetia and Collin,
                    Matthew and Manz, Markus G. and McClain, Kenneth and
                    Merad, Miriam and Allen, Carl E.},
  Title           = {{BRAF}-{V600E} expression in precursor versus
                    differentiated dendritic cells defines clinically
                    distinct {LCH} risk groups},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2014},
  author+an:default = {1=equal;2=equal;3=equal},
  Addendum        = equal,
  DOI             = {10.1084/jem.20130977},
  Keywords        = {Berres-Selection},
  Number          = {4},
  Pages           = {669--683},
  ShortJournal    = {JEM},
  Volume          = {211}
}

@Article{Berres:480482,
  Author          = {Berres, Marie-Luise and Asmacher, Sonja and Lehmann,
                    Jennifer and Jansen, Christian and Görtzen, Jan and
                    Klein, Sabine and Meyer, Carsten and Strunk, Holger M.
                    and Fimmers, Rolf and Tacke, Frank and Strassburg,
                    Christian P. and Trautwein, Christian and Sauerbruch,
                    Tilman and Wasmuth, Hermann Elard and Trebicka, Jonel},
  Title           = {{CXCL9} is a prognostic marker in patients with liver
                    cirrhosis receiving transjugular intrahepatic
                    portosystemic shunt},
  JournalTitle    = {J. Hepatol.},
  Date            = {2015},
  DOI             = {10.1016/j.jhep.2014.09.032},
  Number          = {2},
  Pages           = {332--339},
  Volume          = {62}
}

@Article{Bettermann:175688,
  Author          = {Bettermann, Kira and Vucur, Mihael and Haybaeck,
                    Johannes and Koppe, Christiane and Janssen, Jörn and
                    Heymann, Felix and Weber, Achim and Weiskirchen, Ralf and
                    Liedtke, Christian and Gassler, Nikolaus and Müller,
                    Michael and de Vos, Rita and Wolf, Monika Julia and
                    Boege, Yannick and Seleznik, Gitta Maria and Zeller,
                    Nicolas and Erny, Daniel and Fuchs, Thomas and Zoller,
                    Stefan and Cairo, Stefano and Buendia, Marie-Annick and
                    Prinz, Marco and Akira, Shizuo and Tacke, Frank and
                    Heikenwalder, Mathias and Trautwein, Christian and
                    Luedde, Tom},
  Title           = {{TAK1} Suppresses a {NEMO}-Dependent but
                    {NF}-{κB}-Independent Pathway to Liver Cancer},
  JournalTitle    = {Cancer Cell},
  Date            = {2010},
  DOI             = {10.1016/j.ccr.2010.03.021},
  Keywords        = {Liedtke-Selection,Lüdde-Selection},
  Number          = {5},
  Pages           = {481--496},
  Volume          = {17}
}

@Article{Bhargava2022-cc,
  Author          = {Bhargava, Shruti and Merckelbach, Erik and Noels, Heidi
                    and Vohra, Ashima and Jankowski, Joachim},
  Title           = {Homeostasis in the Gut Microbiota in Chronic Kidney
                    Disease},
  JournalTitle    = {Toxins},
  Date            = {2022},
  DOI             = {10.3390/toxins14100648},
  Number          = {10},
  Pages           = {648},
  Volume          = {14}
}

@Article{Soppert2022-fd,
  Author          = {Soppert, J. and Brandt, E. B. and Heussen, N. M. and
                    Barzakova, E. and Blank, L. and Kuepfer, L. and Hornef,
                    M. W. and Trebicka, J. and Jankowski, J. and Berres, M.
                    L. and Noels, H.},
  Title           = {Blood endotoxin levels as biomarker of non-alcoholic
                    fatty liver disease: {A} systematic review and
                    meta-analysis},
  Keywords = {Barzakova-Selection},
  PubState        = {accepted},
  journaltitle = {Clin. Gastroenterol. Hepatol.},
  date = {2022}
}

@Article{Bhargava2022-yc,
  Author          = {Bhargava, Shruti and de la Puente-Secades, Sofia and
                    Schurgers, Leon and Jankowski, Joachim},
  Title           = {Lipids and lipoproteins in cardiovascular diseases: {A}
                    classification},
  JournalTitle    = {Trends Endocrinol. Metab.},
  Date            = {2022},
  DOI             = {10.1016/j.tem.2022.02.001},
  Keywords        = {Jankowski-Selection},
  Number          = {6},
  Pages           = {409--423},
  Volume          = {33}
}

@Article{Biancacci:813421,
  Author          = {Biancacci, Ilaria and Sun, Qingxue and Möckel, Diana
                    and Gremse, Felix and Rosenhain, Stefanie and Kießling,
                    Fabian and Bartneck, Matthias and Hu, Qizhi and
                    Thewissen, Marielle and Storm, Gert and Hennink, Wim E.
                    and Shi, Yang and Rijcken, Cristianne J. F. and Lammers,
                    Twan and Sofias, Alexandros Marios},
  Title           = {Optical imaging of the whole-body to cellular
                    biodistribution of clinical-stage {PEG}-b-p{HPMA}-based
                    core-crosslinked polymeric micelles},
  JournalTitle    = {J. Control. Release},
  Date            = {2020},
  DOI             = {10.1016/j.jconrel.2020.09.046},
  Keywords        = {,CRC1382-Project Q01,CRC1382-Project Q01,CRC1382-Project
                    Q01},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {805--816},
  Volume          = {328}
}

@Article{Biancacci:839980,
  Author          = {Biancacci, Ilaria and De Lorenzi, Federica and Theek,
                    Benjamin and Bai, Xiangyang and May, Jan-Niklas and
                    Consolino, Lorena and Baues, Maike and Moeckel, Diana and
                    Gremse, Felix and Stillfried, Saskia and El Shafei, Asmaa
                    and Benderski, Karina and Azadkhah Shalmani, Armin and
                    Wang, Alec and Momoh, Jeffrey and Peña, Quim and Buhl,
                    Eva Miriam and Buyel, Johannes Felix and Hennink, Wim and
                    Kießling, Fabian and Metselaar, Josbert and Shi, Yang
                    and Lammers, Twan},
  Title           = {Monitoring {EPR} Effect Dynamics during Nanotaxane
                    Treatment with Theranostic Polymeric Micelles},
  JournalTitle    = {Adv. Sci.},
  Date            = {2022},
  DOI             = {10.1002/advs.202103745},
  Keywords        = {,CRC1382-Project Q01,CRC1382-Project Q01},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {2103745}
}

@Article{Welzel2013-eh,
  Author          = {Welzel, Tania M and Graubard, Barry I and Quraishi,
                    Sabah and Zeuzem, Stefan and Davila, Jessica A and
                    El-Serag, Hashem B and McGlynn, Katherine A},
  Title           = {Population-Attributable Fractions of Risk Factors for
                    Hepatocellular Carcinoma in the United States},
  JournalTitle    = {Am. J. Gastroenterol.},
  Date            = {2013},
  DOI             = {10.1038/ajg.2013.160},
  Number          = {8},
  Pages           = {1314--1321},
  Volume          = {108}
}

@Article{Sellin2014-wt,
  Author          = {Sellin, Mikael E. and Müller, Anna A. and Felmy, Boas
                    and Dolowschiak, Tamas and Diard, Médéric and Tardivel,
                    Aubry and Maslowski, Kendle M. and Hardt, Wolf-Dietrich},
  Title           = {Epithelium-Intrinsic {NAIP/NLRC4} Inflammasome Drives
                    Infected Enterocyte Expulsion to Restrict Salmonella
                    Replication in the Intestinal Mucosa},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2014},
  DOI             = {10.1016/j.chom.2014.07.001},
  Number          = {2},
  Pages           = {237--248},
  Volume          = {16}
}

@Article{Birchenough2015-it,
  Author          = {Birchenough, G M H and Johansson, M EV and Gustafsson, J
                    K and Bergström, J H and Hansson, G C},
  Title           = {New developments in goblet cell mucus secretion and
                    function},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2015},
  DOI             = {10.1038/mi.2015.32},
  Number          = {4},
  Pages           = {712--719},
  Volume          = {8}
}

@Article{Birchenough2016,
  Author          = {Birchenough, George M. H. and Nyström, Elisabeth E. L.
                    and Johansson, Malin E. V. and Hansson, Gunnar C.},
  Title           = {A sentinel goblet cell guards the colonic crypt by
                    triggering Nlrp6-dependent Muc2 secretion},
  JournalTitle    = {Science},
  Date            = {2016-24},
  DOI             = {10.1126/science.aaf7419},
  Note            = {PMC5148821},
  Number          = {6293},
  Pages           = {1535--1542},
  Volume          = {352},
  yeardivision    = {winter}
}

@Article{Blachier2013-gi,
  Author          = {Blachier, Martin and Leleu, Henri and
                    Peck-Radosavljevic, Markus and Valla, Dominique-Charles
                    and Roudot-Thoraval, Françoise},
  Title           = {The burden of liver disease in Europe: {A} review of
                    available epidemiological data},
  JournalTitle    = {J. Hepatol.},
  Date            = {2013},
  DOI             = {10.1016/j.jhep.2012.12.005},
  Number          = {3},
  Pages           = {593--608},
  Volume          = {58}
}

@Article{Blank:196155,
  Author          = {Blank, Lars M. and Kuepfer, Lars},
  Title           = {Metabolic flux distributions: {Genetic} information,
                    computational predictions, and experimental validation},
  JournalTitle    = {Appl. Microbiol. Biot.},
  Date            = {2010},
  DOI             = {10.1007/s00253-010-2506-6},
  Number          = {5},
  Pages           = {1243--1255},
  Volume          = {86}
}

@Article{Blank:699199,
  Author          = {Blank, Lars M.},
  Title           = {Let's talk about flux or the importance of
                    (intracellular) reaction rates},
  JournalTitle    = {Microb. Biotechnol.},
  Date            = {2016},
  DOI             = {10.1111/1751-7915.12455},
  Number          = {1},
  Pages           = {28--30},
  Volume          = {10}
}

@Article{Bleriot2021-xc,
  Author          = {Blériot, Camille and Barreby, Emelie and Dunsmore,
                    Garett and Ballaire, Raphaelle and Chakarov, Svetoslav
                    and Ficht, Xenia and De Simone, Giorgia and Andreata,
                    Francesco and Fumagalli, Valeria and Guo, Wei and Wan,
                    Guochen and Gessain, Gregoire and Khalilnezhad, Ahad and
                    Zhang, Xiao Meng and Ang, Nicholas and Chen, Ping and
                    Morgantini, Cecilia and Azzimato, Valerio and Kong, Wan
                    Ting and Liu, Zhaoyuan and Pai, Rhea and Lum, Josephine
                    and Shihui, Foo and Low, Ivy and Xu, Connie and Malleret,
                    Benoit and Kairi, Muhammad Faris Mohd and Balachander,
                    Akhila and Cexus, Olivier and Larbi, Anis and Lee,
                    Bernett and Newell, Evan W. and Ng, Lai Guan and Phoo,
                    Wint Wint and Sobota, Radoslaw M. and Sharma, Ankur and
                    Howland, Shanshan W. and Chen, Jinmiao and Bajenoff, Marc
                    and Yvan-Charvet, Laurent and Venteclef, Nicolas and
                    Iannacone, Matteo and Aouadi, Myriam and Ginhoux,
                    Florent},
  Title           = {A subset of Kupffer cells regulates metabolism through
                    the expression of {CD36}},
  JournalTitle    = {Immunity},
  Date            = {2021},
  DOI             = {10.1016/j.immuni.2021.08.006},
  Number          = {9},
  Pages           = {2101--2116.e6},
  Volume          = {54}
}

@Article{Blesken2020-tr,
  Author          = {Blesken, Christian C. and Bator, Isabel and Eberlein,
                    Christian and Heipieper, Hermann J. and Tiso, Till and
                    Blank, Lars M.},
  Title           = {Genetic Cell-Surface Modification for Optimized Foam
                    Fractionation},
  JournalTitle    = {Front. Bioeng. Biotechnol.},
  Date            = {2020},
  DOI             = {10.3389/fbioe.2020.572892},
  Keywords        = {Blank-Selection},
  Pages           = {572892},
  Volume          = {8}
}

@Article{Bosch2004-wb,
  Author          = {Bosch, F.Xavier and Ribes, Josepa and Díaz, Mireia and
                    Cléries, Ramon},
  Title           = {Primary liver cancer: {Worldwide} incidence and trends},
  JournalTitle    = {Gastroenterology},
  Date            = {2004},
  DOI             = {10.1053/j.gastro.2004.09.011},
  Number          = {5},
  Pages           = {S5--S16},
  Volume          = {127}
}

@Article{Bossert:788839,
  Author          = {Bossert, Lukas C.},
  Title           = {Mit »biber --tool« Bibliografieeinträge bearbeiten},
  JournalTitle    = {Die TEXnische Komödie},
  Date            = {2020},
  DOI             = {10.5281/zenodo.3784922},
  Options         = {openaccess=auto},
  doi+an:default  = {=openaccess},
  Keywords        = {,CRC1382-Project Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {24--33},
  Volume          = {2}
}

@Article{Dadfar2020-hn,
  Author          = {Dadfar, Seyed Mohammadali and Camozzi, Denise and
                    Darguzyte, Milita and Roemhild, Karolin and Varvarà,
                    Paola and Metselaar, Josbert and Banala, Srinivas and
                    Straub, Marcel and Güvener, Nihan and Engelmann, Ulrich
                    and Slabu, Ioana and Buhl, Miriam and van Leusen, Jan and
                    Kögerler, Paul and Hermanns-Sachweh, Benita and Schulz,
                    Volkmar and Kiessling, Fabian and Lammers, Twan},
  Title           = {Size-isolation of superparamagnetic iron oxide
                    nanoparticles improves {MRI,} {MPI} and hyperthermia
                    performance},
  JournalTitle    = {J. Nanobiotechnology},
  Date            = {2020},
  DOI             = {10.1186/s12951-020-0580-1},
  Number          = {1},
  Pages           = {22},
  Volume          = {18}
}

@Misc{Bossert:834806,
  Author          = {Bossert, Lukas C.},
  Title           = {{CRC}1382 and its {DMP}},
  Date            = {2021},
  DOI             = {10.6084/M9.FIGSHARE.16922557.V1},
  Keywords        = {,CRC1382-Project Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {113879064 Bytes}
}

@Article{BenKhaled2022-db,
  Author          = {Ben Khaled, Najib and Seidensticker, Max and Ricke, Jens
                    and Mayerle, Julia and Oehrle, Bettina and Rössler,
                    Daniel and Teupser, Daniel and Ehmer, Ursula and Bitzer,
                    Michael and Waldschmidt, Dirk and Fuchs, Martin and
                    Reuken, Philipp A and Lange, Christian M and Wege,
                    Henning and Kandulski, Arne and Dechêne, Alexander and
                    Venerito, Marino and Berres, Marie-Luise and Luedde, Tom
                    and Kubisch, Ilja and Reiter, Florian P and De Toni,
                    Enrico N},
  Title           = {Atezolizumab and bevacizumab with transarterial
                    chemoembolization in hepatocellular carcinoma: {The}
                    {DEMAND} trial protocol},
  JournalTitle    = {Future Oncol.},
  Date            = {2022},
  Addendum        = preliminarywork,
  DOI             = {10.2217/fon-2021-1261},
  Number          = {12},
  Pages           = {1423--1435},
  Volume          = {18}
}

@Article{Brandt2022-qh,
  Author          = {Brandt, Elisa F. and Baues, Maike and Wirtz, Theresa H.
                    and May, Jan-Niklas and Fischer, Petra and Beckers, Anika
                    and Schüre, Björn-Carsten and Sahin, Hacer and
                    Trautwein, Christian and Lammers, Twan and Berres,
                    Marie-Luise},
  Title           = {Chemokine {CXCL10} Modulates the Tumor Microenvironment
                    of Fibrosis-Associated Hepatocellular Carcinoma},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2022},
  DOI             = {10.3390/ijms23158112},
  Keywords        = {CXCL10; angiogenesis; chemokine/chemokine receptor
                    network; hepatocellular carcinoma; tumor cell
                    proliferation; tumor microenvironment; tumor-associated
                    immune response},
  Number          = {15},
  Pages           = {8112},
  Volume          = {23}
}

@Article{Brennan2013Chemoreceptor,
  Author          = {Brennan, Caitlin A. and DeLoney-Marino, Cindy R. and
                    Mandel, Mark J.},
  Title           = {Chemoreceptor {VfcA} Mediates Amino Acid Chemotaxis in
                    Vibrio fischeri},
  JournalTitle    = {Appl. Environ. Microbiol.},
  Date            = {2013-03-15},
  DOI             = {10.1128/aem.03794-12},
  Number          = {6},
  Pages           = {1889--1896},
  Volume          = {79}
}

@Article{Brestoff2013Commensal,
  Author          = {Brestoff, Jonathan R and Artis, David},
  Title           = {Commensal bacteria at the interface of host metabolism
                    and the immune system},
  JournalTitle    = {Nat. Immunol.},
  Date            = {2013-07},
  DOI             = {10.1038/ni.2640},
  Number          = {7},
  Pages           = {676--684},
  Volume          = {14}
}

@Article{Brodin2022-fi,
  Author          = {Brodin, Petter},
  Title           = {Immune-microbe interactions early in life: A determinant
                    of health and disease long term},
  JournalTitle    = {Science},
  Date            = {2022},
  DOI             = {10.1126/science.abk2189},
  Number          = {6596},
  Pages           = {945--950},
  Volume          = {376}
}

@Article{Bruneau2021-lg,
  Author          = {Bruneau, Alix and Hundertmark, Jana and Guillot, Adrien
                    and Tacke, Frank},
  Title           = {Molecular and Cellular Mediators of the Gut-Liver Axis
                    in the Progression of Liver Diseases},
  JournalTitle    = {Frontiers in Medicine},
  Date            = {2021},
  DOI             = {10.3389/fmed.2021.725390},
  Pages           = {725390},
  Volume          = {8}
}

@Article{Bruneau2022-mg,
  Author          = {Bruneau, Alix and Guillot, Adrien and Tacke, Frank},
  Title           = {Macrophages in cholangiopathies},
  JournalTitle    = {Curr. Opin. Gastroenterol.},
  Date            = {2021},
  DOI             = {10.1097/mog.0000000000000814},
  Number          = {2},
  Pages           = {114--120},
  Volume          = {38}
}

@Article{Bruns2015,
  Author          = {Bruns, Tony and Zimmermann, Henning W. and Pachnio,
                    Annette and Li, Ka-Kit and Trivedi, Palak J. and
                    Reynolds, Gary and Hubscher, Stefan and Stamataki, Zania
                    and Badenhorst, Paul W. and Weston, Christopher J. and
                    Moss, Paul A. and Adams, David H.},
  Title           = {{CMV} infection of human sinusoidal endothelium
                    regulates hepatic T cell recruitment and activation},
  JournalTitle    = {J. Hepatol.},
  Date            = {2015},
  DOI             = {10.1016/j.jhep.2015.02.046},
  Keywords        = {Bruns-Selection},
  Number          = {1},
  Pages           = {38--49},
  Volume          = {63}
}

@Article{Bajaj2022-gp,
  Author          = {Bajaj, Jasmohan S. and Ng, Siew C. and Schnabl, Bernd},
  Title           = {Promises of microbiome-based therapies},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2021.12.003},
  Keywords        = {cirrhosis; fecal microbiota transplantation;
                    gut-liver-axis; mycobiome},
  Number          = {6},
  Pages           = {1379--1391},
  Volume          = {76}
}

@Article{Bruns2016,
  Author          = {Bruns, Tony and Reuken, Philipp A. and Stengel, Sven and
                    Gerber, Ludmila and Appenrodt, Beate and Schade, Johannes
                    H. and Lammert, Frank and Zeuzem, Stefan and Stallmach,
                    Andreas},
  Title           = {The prognostic significance of bacterial {DNA} in
                    patients with decompensated cirrhosis and suspected
                    infection},
  JournalTitle    = {Liver Int.},
  Date            = {2016},
  DOI             = {10.1111/liv.13095},
  Keywords        = {Bruns-Selection},
  Number          = {8},
  Pages           = {1133--1142},
  Volume          = {36}
}

@Article{Buendgens:803962,
  Author          = {Buendgens, Lukas and Yagmur, Eray and Ginsberg, Axel and
                    Weiskirchen, Ralf and Wirtz, Theresa H. and Jhaisha,
                    Samira Abu and Eisert, Albrecht and Lüdde, Tom and
                    Trautwein, Christian and Tacke, Frank and Koch,
                    Alexander},
  Title           = {Midregional Proadrenomedullin ({MR}pro{ADM}) Serum
                    Levels in Critically Ill Patients Are Associated with
                    Short-Term and Overall Mortality during a Two-Year
                    Follow-Up},
  JournalTitle    = {Mediat. Inflamm.},
  Date            = {2020},
  DOI             = {10.1155/2020/7184803},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project B05,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {7184803},
  Volume          = {2020}
}

@Article{Bui2016-gv,
  Author          = {Bui, Thi Phuong Nam and Shetty, Sudarshan Anand and
                    Lagkouvardos, Ilias and Ritari, Jarmo and Chamlagain,
                    Bhawani and Douillard, François P and Paulin, Lars and
                    Piironen, Vieno and Clavel, Thomas and Plugge, Caroline M
                    and de Vos, Willem M},
  Title           = {Comparative genomics and physiology of the
                    butyrate-producing bacterium Intestinimonas
                    butyriciproducens},
  JournalTitle    = {Environ. Microbiol. Rep.},
  Date            = {2016},
  DOI             = {10.1111/1758-2229.12483},
  Number          = {6},
  Pages           = {1024--1037},
  Volume          = {8}
}

@Article{Bzyl:196364,
  Author          = {Bzyl, Jessica and Palmowski, Moritz and Rix, Anne and
                    Arns, Susanne and Hyvelin, Jean-Marc and Pochon, Sibylle
                    and Ehling, Josef and Schrading, Simone and Kiessling,
                    Fabian and Lederle, Wiltrud},
  Title           = {The high angiogenic activity in very early breast cancer
                    enables reliable imaging with {VEGFR2}-targeted
                    microbubbles {(BR55)}},
  JournalTitle    = {Eur. Radiol.},
  Date            = {2012},
  DOI             = {10.1007/s00330-012-2594-z},
  Number          = {2},
  Pages           = {468--475},
  Volume          = {23}
}

@Article{Cappuyns2022-ip,
  Author          = {Cappuyns, Sarah and Llovet, Josep M.},
  Title           = {Combination Therapies for Advanced Hepatocellular
                    Carcinoma: {Biomarkers} and Unmet Needs},
  JournalTitle    = {Clin. Cancer Res.},
  Date            = {2022},
  DOI             = {10.1158/1078-0432.ccr-22-1213},
  Number          = {16},
  Pages           = {3405--3407},
  Volume          = {28}
}

@Article{Cadamuro2020-nw,
  Author          = {Cadamuro, Massimiliano and Girardi, Noemi and Gores,
                    Gregory J. and Strazzabosco, Mario and Fabris, Luca},
  Title           = {The Emerging Role of Macrophages in Chronic
                    Cholangiopathies Featuring Biliary Fibrosis: {An}
                    Attractive Therapeutic Target for Orphan Diseases},
  JournalTitle    = {Front. Med. (Lausanne)},
  Date            = {2020},
  DOI             = {10.3389/fmed.2020.00115},
  Keywords        = {biliary repair; cholangiocyte; congenital hepatic
                    fibrosis; monocyte; primary sclerosing cholangitis},
  Pages           = {115},
  Volume          = {7}
}

@Article{Campbell2020-pj,
  Author          = {Campbell, Clarissa and McKenney, Peter T. and
                    Konstantinovsky, Daniel and Isaeva, Olga I. and Schizas,
                    Michail and Verter, Jacob and Mai, Cheryl and Jin,
                    Wen-Bing and Guo, Chun-Jun and Violante, Sara and Ramos,
                    Ruben J. and Cross, Justin R. and Kadaveru, Krishna and
                    Hambor, John and Rudensky, Alexander Y.},
  Title           = {Bacterial metabolism of bile acids promotes generation
                    of peripheral regulatory T cells},
  JournalTitle    = {Nature},
  Date            = {2020},
  DOI             = {10.1038/s41586-020-2193-0},
  Number          = {7809},
  Pages           = {475--479},
  Volume          = {581}
}

@Article{Cani2022-wz,
  Author          = {Cani, Patrice D and Depommier, Clara and Derrien, Muriel
                    and Everard, Amandine and de Vos, Willem M},
  Title           = {Akkermansia muciniphila: paradigm for next-generation
                    beneficial microorganisms},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2022},
  DOI             = {10.1038/s41575-022-00631-9},
  Number          = {10},
  Pages           = {625--637},
  Volume          = {19}
}

@Article{Cerovic2009,
  Author          = {Cerovic, Vuk and Jenkins, Christopher D. and Barnes,
                    Andrew G. C. and Milling, Simon W. F. and MacPherson, G.
                    Gordon and Klavinskis, Linda S.},
  Title           = {Hyporesponsiveness of Intestinal Dendritic Cells to
                    {TLR} Stimulation Is Limited to {TLR4}},
  JournalTitle    = {J. Immunol.},
  Date            = {2009},
  DOI             = {10.4049/jimmunol.0802318},
  Keywords        = {Cerovic-Selection},
  Number          = {4},
  Pages           = {2405--2415},
  Volume          = {182}
}

@Article{Cerovic2012,
  Author          = {Cerovic, V and Houston, S A and Scott, C L and
                    Aumeunier, A and Yrlid, U and Mowat, A M and Milling, S W
                    F},
  Title           = {Intestinal {CD103−} dendritic cells migrate in lymph
                    and prime effector T cells},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2012},
  DOI             = {10.1038/mi.2012.53},
  ids             = {cerovic2013a},
  Keywords        = {Cerovic-Selection},
  Number          = {1},
  Pages           = {104--113},
  Volume          = {6}
}

@Article{Cerovic2014,
  Author          = {Cerovic, Vuk and Bain, Calum C. and Mowat, Allan M. and
                    Milling, Simon W.F.},
  Title           = {Intestinal macrophages and dendritic cells: {What's} the
                    difference?},
  JournalTitle    = {Trends Immunol.},
  Date            = {2014},
  DOI             = {10.1016/j.it.2014.04.003},
  Keywords        = {Cerovic-Selection},
  Number          = {6},
  Pages           = {270--277},
  Volume          = {35}
}

@Article{Chaban2015flagellum,
  Author          = {Chaban, Bonnie and Hughes, H. Velocity and Beeby,
                    Morgan},
  Title           = {The flagellum in bacterial pathogens: {For} motility and
                    a whole lot more},
  JournalTitle    = {Semin. Cell Dev. Biol.},
  Date            = {2015-10},
  DOI             = {10.1016/j.semcdb.2015.10.032},
  Pages           = {91--103},
  Volume          = {46}
}

@Article{Chadchan2019-kv,
  Author          = {Chadchan, Sangappa B and Cheng, Meng and Parnell,
                    Lindsay A and Yin, Yin and Schriefer, Andrew and
                    Mysorekar, Indira U and Kommagani, Ramakrishna},
  Title           = {Antibiotic therapy with metronidazole reduces
                    endometriosis disease progression in mice: a potential
                    role for gut microbiota},
  JournalTitle    = {Hum. Reprod.},
  Date            = {2019},
  DOI             = {10.1093/humrep/dez041},
  Keywords        = {endometriosis; gut bacteria; inflammation;
                    metronidazole; microbiome},
  Number          = {6},
  Pages           = {1106--1116},
  Volume          = {34}
}

@Article{Chakarov2022-ms,
  Author          = {Chakarov, Svetoslav and Blériot, Camille and Ginhoux,
                    Florent},
  Title           = {Role of adipose tissue macrophages in obesity-related
                    disorders},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2022},
  DOI             = {10.1084/jem.20211948},
  Number          = {7},
  Volume          = {219}
}

@Article{Chassaing2014Intestinal,
  Author          = {Chassaing, Benoit and Ley, Ruth E. and Gewirtz, Andrew
                    T.},
  Title           = {Intestinal Epithelial Cell Toll-like Receptor 5
                    Regulates the Intestinal Microbiota to Prevent Low-Grade
                    Inflammation and Metabolic Syndrome in Mice},
  JournalTitle    = {Gastroenterology},
  Date            = {2014-12},
  DOI             = {10.1053/j.gastro.2014.08.033},
  Number          = {6},
  Pages           = {1363--1377.e17},
  Volume          = {147}
}

@Article{Chassaing2015Dietary,
  Author          = {Chassaing, Benoit and Koren, Omry and Goodrich, Julia K.
                    and Poole, Angela C. and Srinivasan, Shanthi and Ley,
                    Ruth E. and Gewirtz, Andrew T.},
  Title           = {Dietary emulsifiers impact the mouse gut microbiota
                    promoting colitis and metabolic syndrome},
  JournalTitle    = {Nature},
  Date            = {2015-03-05},
  DOI             = {10.1038/nature14232},
  Number          = {7541},
  Pages           = {92--96},
  Volume          = {519}
}

@Article{Chassaing2017Dietary,
  Author          = {Chassaing, Benoit and Van de Wiele, Tom and De Bodt,
                    Jana and Marzorati, Massimo and Gewirtz, Andrew T},
  Title           = {Dietary emulsifiers directly alter human microbiota
                    composition and gene expression ex vivo potentiating
                    intestinal inflammation},
  JournalTitle    = {Gut},
  Date            = {2017-08},
  DOI             = {10.1136/gutjnl-2016-313099},
  Number          = {8},
  Pages           = {1414--1427},
  Volume          = {66}
}

@Article{Chassin2010,
  Author          = {Chassin, Cécilia and Kocur, Magdalena and Pott, Johanna
                    and Duerr, Claudia U. and Gütle, Dominique and Lotz,
                    Michael and Hornef, Mathias W.},
  Title           = {{miR}-146a Mediates Protective Innate Immune Tolerance
                    in the Neonate Intestine},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2010},
  DOI             = {10.1016/j.chom.2010.09.005},
  ids             = {Chassin2010-by,chassin2010a},
  Keywords        = {Hornef-Selection},
  Number          = {4},
  Pages           = {358--368},
  Volume          = {8}
}

@Article{Chassin2012,
  Author          = {Chassin, Cécilia and Hempel, Cordelia and Stockinger,
                    Silvia and Dupont, Aline and Kübler, Joachim F. and
                    Wedemeyer, Jochen and Vandewalle, Alain and Hornef,
                    Mathias W.},
  Title           = {{MicroRNA‐146a‐mediated} downregulation of {IRAK1}
                    protects mouse and human small intestine against
                    ischemia/reperfusion injury},
  JournalTitle    = {EMBO Mol. Med.},
  Date            = {2012},
  DOI             = {10.1002/emmm.201201298},
  Keywords        = {Hornef-Selection},
  Number          = {12},
  Pages           = {1308--1319},
  Volume          = {4}
}

@Article{Chen:572518,
  Author          = {Chen, Yu and Guldiken, Nurdan and Spurny, Manuela and
                    Mohammed, Hawraman HA and Haybaeck, Johannes and
                    Pollheimer, Marion J and Fickert, Peter and Gassler,
                    Nikolaus and Jeon, Min Kyung and Trautwein, Christian and
                    Strnad, Pavel},
  Title           = {Loss of keratin 19 favours the development of
                    cholestatic liver disease through decreased ductular
                    reaction},
  JournalTitle    = {J. Pathol.},
  Date            = {2015},
  DOI             = {10.1002/path.4580},
  Keywords        = {Guldiken-Selection},
  Number          = {3},
  Pages           = {343--354},
  Subtitle        = {K19 and ductular reaction},
  Volume          = {237}
}

@Article{Clahsen:465151,
  Author          = {Clahsen, Thomas and Pabst, Oliver and Tenbrock, Klaus
                    and Schippers, Angela and Wagner, Norbert},
  Title           = {Localization of dendritic cells in the gut epithelium
                    requires {MAdCAM}-1},
  JournalTitle    = {Clin. Immunol.},
  Date            = {2015},
  Addendum        = sharedlast,
  author+an:default = {4=sharedLast;5=sharedLast},
  DOI             = {10.1016/j.clim.2014.11.005},
  Keywords        = {Schippers-Selection,Wagner-Selection},
  Number          = {1},
  Pages           = {74--84},
  Volume          = {156}
}

@Article{Clavel:836462,
  Author          = {Clavel, Thomas and Horz, Hans-Peter and Segata, Nicola
                    and Vehreschild, Maria},
  Title           = {Next steps after 15 stimulating years of human gut
                    microbiome research},
  JournalTitle    = {Microbial biotechnology},
  Date            = {2022},
  DOI             = {10.1111/1751-7915.13970},
  Keywords        = {,CRC1382-Project A05,CRC1382-Project Q02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {164--175},
  Volume          = {15}
}

@Article{Clocchiatti2016,
  Author          = {Clocchiatti, Andrea and Cora, Elisa and Zhang, Yosra and
                    Dotto, G. Paolo},
  Title           = {Sexual dimorphism in cancer},
  JournalTitle    = {Nat. Rev. Cancer},
  Date            = {2016},
  DOI             = {10.1038/nrc.2016.30},
  Number          = {5},
  Pages           = {330--339},
  Volume          = {16}
}

@Article{Coelen2018-da,
  Author          = {Coelen, Robert J S and Roos, Eva and Wiggers, Jimme K
                    and Besselink, Marc G and Buis, Carlijn I and Busch,
                    Olivier R C and Dejong, Cornelis H C and van Delden, Otto
                    M and van Eijck, Casper H J and Fockens, Paul and Gouma,
                    Dirk J and Koerkamp, Bas Groot and de Haan, Michiel W and
                    van Hooft, Jeanin E and IJzermans, Jan N M and Kater, G
                    Matthijs and Koornstra, Jan J and van Lienden, Krijn P
                    and Moelker, Adriaan and Olde Damink, Steven W. M. and
                    Poley, Jan-Werner and Porte, Robert J and de Ridder,
                    Rogier J and Verheij, Joanne and van Woerden, Victor and
                    Rauws, Erik A J and Dijkgraaf, Marcel G W and van Gulik,
                    Thomas M},
  Title           = {Endoscopic versus percutaneous biliary drainage in
                    patients with resectable perihilar cholangiocarcinoma:
                    {A} multicentre, randomised controlled trial},
  JournalTitle    = {Lancet Gastroenterol. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/s2468-1253(18)30234-6},
  Number          = {10},
  Pages           = {681--690},
  Volume          = {3}
}

@Article{Colin2021Multiple,
  Author          = {Colin, Remy and Ni, Bin and Laganenka, Leanid and
                    Sourjik, Victor},
  Title           = {Multiple functions of flagellar motility and chemotaxis
                    in bacterial physiology},
  JournalTitle    = {FEMS Microbiol. Rev.},
  Date            = {2021-11-23},
  DOI             = {10.1093/femsre/fuab038},
  Number          = {6},
  Pages           = {fuab038},
  Volume          = {45}
}

@Article{Comstock2020,
  Author          = {Comstock, Christopher E. and Gatsonis, Constantine and
                    Newstead, Gillian M. and Snyder, Bradley S. and Gareen,
                    Ilana F. and Bergin, Jennifer T. and Rahbar, Habib and
                    Sung, Janice S. and Jacobs, Christina and Harvey,
                    Jennifer A. and Nicholson, Mary H. and Ward, Robert C.
                    and Holt, Jacqueline and Prather, Andrew and Miller,
                    Kathy D. and Schnall, Mitchell D. and Kuhl, Christiane
                    K.},
  Title           = {Comparison of Abbreviated Breast {MRI} vs Digital Breast
                    Tomosynthesis for Breast Cancer Detection Among Women
                    With Dense Breasts Undergoing Screening},
  JournalTitle    = {JAMA},
  Date            = {2020},
  DOI             = {10.1001/jama.2020.0572},
  Keywords        = {Kuhl-Selection},
  Number          = {8},
  Pages           = {746},
  Volume          = {323}
}

@Article{Vaishnava2011-vl,
  Author          = {Vaishnava, Shipra and Yamamoto, Miwako and Severson,
                    Kari M. and Ruhn, Kelly A. and Yu, Xiaofei and Koren,
                    Omry and Ley, Ruth and Wakeland, Edward K. and Hooper,
                    Lora V.},
  Title           = {The Antibacterial Lectin {RegIIIγ} Promotes the Spatial
                    Segregation of Microbiota and Host in the Intestine},
  JournalTitle    = {Science},
  Date            = {2011},
  DOI             = {10.1126/science.1209791},
  Number          = {6053},
  Pages           = {255--258},
  Volume          = {334}
}

@Article{Constant2021-wa,
  Author          = {Constant, David A and Nice, Timothy J and Rauch,
                    Isabella},
  Title           = {Innate immune sensing by epithelial barriers},
  JournalTitle    = {Curr. Opin. Immunol.},
  Date            = {2021},
  DOI             = {10.1016/j.coi.2021.07.014},
  Pages           = {1--8},
  Volume          = {73}
}

@Article{Constantino2018Bipolar,
  Author          = {Constantino, Maira A. and Jabbarzadeh, Mehdi and Fu,
                    Henry C. and Shen, Zeli and Fox, James G. and
                    Haesebrouck, Freddy and Linden, Sara K. and Bansil,
                    Rama},
  Title           = {Bipolar lophotrichous {Helicobacter} suis combine
                    extended and wrapped flagella bundles to exhibit multiple
                    modes of motility},
  JournalTitle    = {Sci. Rep.},
  Date            = {2018-12},
  DOI             = {10.1038/s41598-018-32686-7},
  Note            = {[Online; accessed 2020-03-09]},
  Number          = {1},
  Volume          = {8}
}

@Article{Cording2014-vj,
  Author          = {Cording, S and Wahl, B and Kulkarni, D and Chopra, H and
                    Pezoldt, J and Buettner, M and Dummer, A and Hadis, U and
                    Heimesaat, M and Bereswill, S and Falk, C and Bode, U and
                    Hamann, A and Fleissner, D and Huehn, J and Pabst, O},
  Title           = {The intestinal micro-environment imprints stromal cells
                    to promote efficient Treg induction in gut-draining lymph
                    nodes},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2013},
  DOI             = {10.1038/mi.2013.54},
  Number          = {2},
  Pages           = {359--368},
  Volume          = {7}
}

@Article{Cordes:728796,
  Author          = {Cordes, Henrik and Thiel, Christoph and Baier, Vanessa
                    and Blank, Lars M. and Kuepfer, Lars},
  Title           = {Integration of genome-scale metabolic networks into
                    whole-body {PBPK} models shows phenotype-specific cases
                    of drug-induced metabolic perturbation},
  JournalTitle    = {npj Syst. Biol. Appl.},
  Date            = {2018},
  DOI             = {10.1038/s41540-018-0048-1},
  Keywords        = {Blank-Selection,Küpfer-Selection},
  Number          = {1},
  Pages           = {10},
  Volume          = {4}
}

@Article{Cremonese:803969,
  Author          = {Cremonese, Carla and Schierwagen, Robert and Uschner,
                    Frank Erhard and Torres, Sandra and Tyc, Olaf and Ortiz,
                    Cristina and Schulz, Martin and Queck, Alexander and
                    Kristiansen, Glen and Bader, Michael and Sauerbruch,
                    Tilman and Weiskirchen, Ralf and Walther, Thomas and
                    Trebicka, Jonel and Klein, Sabine},
  Title           = {Short-Term Western Diet Aggravates Non-Alcoholic Fatty
                    Liver Disease ({NAFLD}) With Portal Hypertension in
                    {TGR}(m{REN}2)27 Rats},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2020},
  DOI             = {10.3390/ijms21093308},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project A09,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {9},
  Pages           = {3308},
  Volume          = {21}
}

@Article{Cubero:462138,
  Author          = {Cubero, Francisco Javier and Zhao, Gang and Nevzorova,
                    Yulia A. and Hatting, Maximilian and Al Masaoudi, Malika
                    and Verdier, Julien and Peng, Jin and Schaefer, Frederik
                    M. and Hermanns, Nadine and Boekschoten, Mark V. and
                    Grouls, Christoph and Gassler, Nikolaus and Kiessling,
                    Fabian and Muller, Michael and Davis, Roger J. and
                    Liedtke, Christian and Trautwein, Christian},
  Title           = {Haematopoietic cell-derived Jnk1 is crucial for chronic
                    inflammation and carcinogenesis in an experimental model
                    of liver injury},
  JournalTitle    = {J. Hepatol.},
  Date            = {2015},
  DOI             = {10.1016/j.jhep.2014.08.029},
  Keywords        = {Hatting-Selection,Nevzorova-Selection},
  Number          = {1},
  Pages           = {140--149},
  Volume          = {62}
}

@Article{Cubero:685005,
  Author          = {Cubero, Francisco Javier and Zoubek, Miguel Eugenio and
                    Hu, Wei and Peng, Jin and Zhao, Gang and Nevzorova, Yulia
                    A. and Al Masaoudi, Malika and Bechmann, Lars P. and
                    Boekschoten, Mark V. and Muller, Michael and Preisinger,
                    Christian and Gassler, Nikolaus and Canbay, Ali E. and
                    Luedde, Tom and Davis, Roger J. and Liedtke, Christian
                    and Trautwein, Christian},
  Title           = {Combined Activities of {JNK1} and {JNK2} in Hepatocytes
                    Protect Against Toxic Liver Injury},
  JournalTitle    = {Gastroenterology},
  Date            = {2016},
  DOI             = {10.1053/j.gastro.2015.12.019},
  ids             = {cubero2016a},
  Number          = {4},
  Pages           = {968--981},
  Volume          = {150}
}

@Article{Cubero:753992,
  Author          = {Cubero, Francisco Javier and Peng, Jin and Liao, Lijun
                    and Su, Huan and Zhao, Gang and Zoubek, Miguel Eugenio
                    and Macías-Rodríguez, Ricardo and Ruiz-Margain, Astrid
                    and Reißing, Johanna and Zimmermann, Henning W. and
                    Gassler, Nikolaus and Luedde, Tom and Liedtke, Christian
                    and Hatting, Maximilian and Trautwein, Christian},
  Title           = {Inactivation of caspase 8 in liver parenchymal cells
                    confers protection against murine obstructive
                    cholestasis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/j.jhep.2018.08.015},
  Number          = {6},
  Pages           = {1326--1334},
  Volume          = {69}
}

@Article{Cullaro:834282,
  Author          = {Cullaro, Giuseppe and Sharma, Rajani and Trebicka, Jonel
                    and Cárdenas, Andrés and Verna, Elizabeth C.},
  Title           = {Precipitants of Acute-on-Chronic Liver Failure: An
                    Opportunity for Preventative Measures to Improve
                    Outcomes},
  JournalTitle    = {Liver Transplant.},
  Date            = {2020},
  DOI             = {10.1002/lt.25678},
  Keywords        = {,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {283--293},
  Volume          = {26}
}

@Article{Cullender2013Innate,
  Author          = {Cullender, Tyler C. and Chassaing, Benoit and Janzon,
                    Anders and Kumar, Krithika and Muller, Catherine E. and
                    Werner, Jeffrey J. and Angenent, Largus T. and Bell, M.
                    Elizabeth and Hay, Anthony G. and Peterson, Daniel A. and
                    Walter, Jens and Vijay-Kumar, Matam and Gewirtz, Andrew
                    T. and Ley, Ruth E.},
  Title           = {Innate and Adaptive Immunity Interact to Quench
                    Microbiome Flagellar Motility in the Gut},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2013-11},
  DOI             = {10.1016/j.chom.2013.10.009},
  Number          = {5},
  Pages           = {571--581},
  Volume          = {14}
}

@Article{Daims2015,
  Author          = {Daims, Holger and Lebedeva, Elena V. and Pjevac, Petra
                    and Han, Ping and Herbold, Craig and Albertsen, Mads and
                    Jehmlich, Nico and Palatinszky, Marton and Vierheilig,
                    Julia and Bulaev, Alexandr and Kirkegaard, Rasmus H. and
                    von Bergen, Martin and Rattei, Thomas and Bendinger,
                    Bernd and Nielsen, Per H. and Wagner, Michael},
  Title           = {Complete nitrification by Nitrospira bacteria},
  JournalTitle    = {Nature},
  Date            = {2015},
  DOI             = {10.1038/nature16461},
  Number          = {7583},
  Pages           = {504--509},
  Volume          = {528}
}

@Article{Damink2003,
  Author          = {Olde Damink, Steven W. M. and Jalan, Rajiv and Deutz,
                    Nicolaas E. P. and Redhead, Doris N. and Dejong, Cornelis
                    H. C. and Hynd, Paula and Hayes, Rosy A. Jalan Peter C.
                    and Soeters, Peter B.},
  Title           = {The kidney plays a major role in the hyperammonemia seen
                    after simulated or actual {GI} bleeding in patients with
                    cirrhosis},
  JournalTitle    = {Hepatology},
  Date            = {2003},
  DOI             = {10.1053/jhep.2003.50221},
  Number          = {6},
  Pages           = {1277--1285},
  Volume          = {37}
}

@Article{Daniel2013,
  Author          = {Daniel, Hannelore and Gholami, Amin Moghaddas and Berry,
                    David and Desmarchelier, Charles and Hahne, Hannes and
                    Loh, Gunnar and Mondot, Stanislas and Lepage, Patricia
                    and Rothballer, Michael and Walker, Alesia and Böhm,
                    Christoph and Wenning, Mareike and Wagner, Michael and
                    Blaut, Michael and Schmitt-Kopplin, Philippe and Kuster,
                    Bernhard and Haller, Dirk and Clavel, Thomas},
  Title           = {High-fat diet alters gut microbiota physiology in mice},
  JournalTitle    = {ISME J.},
  Date            = {2013},
  DOI             = {10.1038/ismej.2013.155},
  Number          = {2},
  Pages           = {295--308},
  Volume          = {8}
}

@Article{Daniel2021H,
  Author          = {Daniel, Noëmie and Lécuyer, Emelyne and Chassaing,
                    Benoit},
  Title           = {Host/microbiota interactions in health and
                    {diseases—Time} for mucosal microbiology!},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2021-09},
  DOI             = {10.1038/s41385-021-00383-w},
  Number          = {5},
  Pages           = {1006--1016},
  Volume          = {14}
}

@Article{DeMuynck2021GutLiver,
  Author          = {De Muynck, Kevin and Vanderborght, Bart and Van
                    Vlierberghe, Hans and Devisscher, Lindsey},
  Title           = {The {Gut–Liver} Axis in Chronic Liver Disease: {A}
                    Macrophage Perspective},
  JournalTitle    = {Cells},
  Date            = {2021-10-30},
  DOI             = {10.3390/cells10112959},
  Number          = {11},
  Pages           = {2959},
  Volume          = {10}
}

@Article{DeSantaBarbara2003-yd,
  Author          = {de Santa Barbara, P. and van den Brink, G. R. and
                    Roberts, D. J.},
  Title           = {Development and differentiation of the intestinal
                    epithelium},
  JournalTitle    = {Cell. Mol. Life Sci.},
  Date            = {2003},
  DOI             = {10.1007/s00018-003-2289-3},
  ids             = {De_Santa_Barbara2003-yd},
  Number          = {7},
  Pages           = {1322--1332},
  Volume          = {60}
}

@Article{De_Aguiar_Vallim2013-ic,
  Author          = {de Aguiar Vallim, Thomas Q. and Tarling, Elizabeth J.
                    and Edwards, Peter A.},
  Title           = {Pleiotropic Roles of Bile Acids in Metabolism},
  JournalTitle    = {Cell Metab.},
  Date            = {2013},
  DOI             = {10.1016/j.cmet.2013.03.013},
  Number          = {5},
  Pages           = {657--669},
  Volume          = {17}
}

@Article{De_Castilhos2021-al,
  Author          = {de Castilhos, Juliana and Zamir, Eli and Hippchen,
                    Theresa and Rohrbach, Roman and Schmidt, Sabine and
                    Hengler, Silvana and Schumacher, Hanna and Neubauer,
                    Melanie and Kunz, Sabrina and Müller-Esch, Tonia and
                    Hiergeist, Andreas and Gessner, André and Khalid, Dina
                    and Gaiser, Rogier and Cullin, Nyssa and Papagiannarou,
                    Stamatia M and Beuthien-Baumann, Bettina and Krämer,
                    Alwin and Bartenschlager, Ralf and Jäger, Dirk and
                    Müller, Michael and Herth, Felix and Duerschmied, Daniel
                    and Schneider, Jochen and Schmid, Roland M and Eberhardt,
                    Johann F and Khodamoradi, Yascha and Vehreschild, Maria
                    J. G. T. and Teufel, Andreas and Ebert, Matthias P and
                    Hau, Peter and Salzberger, Bernd and Schnitzler, Paul and
                    Poeck, Hendrik and Elinav, Eran and Merle, Uta and
                    Stein-Thoeringer, Christoph K},
  Title           = {Severe dysbiosis and specific Haemophilus and Neisseria
                    signatures as hallmarks of the oropharyngeal microbiome
                    in critically ill {COVID-19} patients},
  JournalTitle    = {Clin. Infect. Dis.},
  Date            = {2021},
  DOI             = {10.1093/cid/ciab902},
  Keywords        = {Vehreschild-Selection}
}

@Article{De_Haan2021-qk,
  Author          = {de Haan, Lianne R. and Verheij, Joanne and van Golen,
                    Rowan F. and Horneffer-van der Sluis, Verena and Lewis,
                    Matthew R. and Beuers, Ulrich H. W. and van Gulik, Thomas
                    M. and Olde Damink, Steven W. M. and Schaap, Frank G. and
                    Heger, Michal and Olthof, Pim B.},
  Title           = {Unaltered Liver Regeneration in Post-Cholestatic Rats
                    Treated with the {FXR} Agonist Obeticholic Acid},
  JournalTitle    = {Biomolecules},
  Date            = {2021},
  DOI             = {10.3390/biom11020260},
  Number          = {2},
  Pages           = {260},
  Volume          = {11}
}

@Article{Demir2019-jx,
  Author          = {Demir, Esra and Ozkan, Hanise and Seckin, Kerem Doga and
                    Sahtiyanc{ı}, Berrak and Demir, Bulent and Tabak, Omur
                    and Kumbasar, Abdülbaki and Uzun, Hafize},
  Title           = {Plasma zonulin levels as a non-invasive biomarker of
                    intestinal permeability in women with gestational
                    diabetes mellitus},
  JournalTitle    = {Biomolecules},
  Date            = {2019},
  DOI             = {10.3390/biom9010024},
  Keywords        = {gestational diabetes mellitus; intestinal permeability;
                    pregnancy; zonulin},
  Number          = {1},
  Pages           = {24},
  Volume          = {9}
}

@Article{Depner:233802,
  Author          = {Depner, Sofia and Lederle, Wiltrud and Gutschalk,
                    Claudia and Linde, Nina and Zajonz, Alexandra and
                    Mueller, Margareta M.},
  Title           = {Cell type specific interleukin-6 induced responses in
                    tumor keratinocytes and stromal fibroblasts are essential
                    for invasive growth},
  JournalTitle    = {Int. J. Cancer},
  Date            = {2014},
  DOI             = {10.1002/ijc.27951},
  Number          = {3},
  Pages           = {551--562},
  Subtitle        = {Cell type specific IL-6 responses in tumor and stromal
                    cells promote invasive growth},
  Volume          = {135}
}

@Article{Paik2022-xu,
  Author          = {Paik, Donggi and Yao, Lina and Zhang, Yancong and Bae,
                    Sena and D’Agostino, Gabriel D. and Zhang, Minghao and
                    Kim, Eunha and Franzosa, Eric A. and Avila-Pacheco,
                    Julian and Bisanz, Jordan E. and Rakowski, Christopher K.
                    and Vlamakis, Hera and Xavier, Ramnik J. and Turnbaugh,
                    Peter J. and Longman, Randy S. and Krout, Michael R. and
                    Clish, Clary B. and Rastinejad, Fraydoon and Huttenhower,
                    Curtis and Huh, Jun R. and Devlin, A. Sloan},
  Title           = {Human gut bacteria produce {ΤΗ17}-modulating bile acid
                    metabolites},
  JournalTitle    = {Nature},
  Date            = {2022},
  DOI             = {10.1038/s41586-022-04480-z},
  Number          = {7903},
  Pages           = {907--912},
  Volume          = {603}
}

@Article{Desalegn:786040,
  Author          = {Desalegn, Girmay and Pabst, Oliver},
  Title           = {Inflammation triggers immediate rather than progressive
                    changes in monocyte differentiation in the small
                    intestine},
  JournalTitle    = {Nat. Commun.},
  Date            = {2019},
  DOI             = {10.1038/s41467-019-11148-2},
  ids             = {Desalegn:786040a},
  Keywords        = {Pabst-Selection,CRC1382-Project B06,CRC1382-Project
                    Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {3229},
  Volume          = {10}
}

@Article{Di_Ciaula2017-rr,
  Author          = {Di Ciaula, Agostino and Garruti, Gabriella and Lunardi
                    Baccetto, Raquel and Molina-Molina, Emilio and Bonfrate,
                    Leonilde and Wang, David Q-H and Portincasa, Piero},
  Title           = {Bile acid physiology},
  JournalTitle    = {Ann. Hepatol.},
  Date            = {2017},
  DOI             = {10.5604/01.3001.0010.5493},
  Keywords        = {Bile acids. Microbiota. FXR. Bile.},
  Number          = {Suppl. 1: s3-105.},
  Pages           = {s4--s14},
  Volume          = {16}
}

@Article{Macpherson2016-cg,
  Author          = {Macpherson, Andrew J. and Heikenwalder, Mathias and
                    Ganal-Vonarburg, Stephanie C.},
  Title           = {The Liver at the Nexus of Host-Microbial Interactions},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2016},
  DOI             = {10.1016/j.chom.2016.10.016},
  Number          = {5},
  Pages           = {561--571},
  Volume          = {20}
}

@Article{Dongiovanni2013-ck,
  Author          = {Dongiovanni, Paola and Donati, Benedetta and Fares,
                    Roberta and Lombardi, Rosa and Mancina, Rosellina
                    Margherita and Romeo, Stefano and Valenti, Luca},
  Title           = {{PNPLA3} {I148M} polymorphism and progressive liver
                    disease},
  JournalTitle    = {World J. Gastroenterol.},
  Date            = {2013},
  DOI             = {10.3748/wjg.v19.i41.6969},
  Number          = {41},
  Pages           = {6969--6978},
  Volume          = {19}
}

@Article{Doleschel2021-sn,
  Author          = {Doleschel, Dennis and Hoff, Sabine and Koletnik, Susanne
                    and Rix, Anne and Zopf, Dieter and Kiessling, Fabian and
                    Lederle, Wiltrud},
  Title           = {Regorafenib enhances anti-{PD1} immunotherapy efficacy
                    in murine colorectal cancers and their combination
                    prevents tumor regrowth},
  JournalTitle    = {J. Exp. Clin. Cancer Res.},
  Date            = {2021},
  DOI             = {10.1186/s13046-021-02043-0},
  Keywords        = {Lederle-Selection},
  Number          = {1},
  Pages           = {288},
  Volume          = {40}
}

@Article{Doleschel:132378,
  Author          = {Doleschel, Dennis and Mundigl, Olaf and Wessner, Axel
                    and Gremse, Felix and Bachmann, Julie and Rodriguez,
                    Agustin and Klingmüller, Ursula and Jarsch, Michael and
                    Kiessling, Fabian and Lederle, Wiltrud},
  Title           = {Targeted Near-Infrared Imaging of the Erythropoietin
                    Receptor in Human Lung Cancer Xenografts},
  JournalTitle    = {J. Nucl. Med.},
  Date            = {2012},
  DOI             = {10.2967/jnumed.111.091124},
  Keywords        = {Lederle-Selection},
  Number          = {2},
  Pages           = {304--311},
  ShortJournal    = {JNM},
  Volume          = {53}
}

@Article{Ernst2014-ar,
  Author          = {Ernst, Thomas M. and Schwinge, Dorothee and Raabe, Nina
                    and Daubmann, Anne and Kaul, Michael G. and Adam, Gerhard
                    and Schramm, Christoph and Ittrich, Harald},
  Title           = {Imaging of the murine biliopancreatic tract at 7 tesla:
                    {Technique} and results in a model of primary sclerosing
                    cholangitis},
  JournalTitle    = {J. Magn. Reson. Imaging},
  Date            = {2013},
  DOI             = {10.1002/jmri.24475},
  Keywords        = {7T; MRCP; PSC; bile duct; cholangiography; mouse},
  Number          = {6},
  Pages           = {1355--1364},
  Subtitle        = {Imaging the Murine Biliopancreatic Tract},
  Volume          = {40}
}

@Article{Doleschel:561370,
  Author          = {Doleschel, Dennis and Rix, Anne and Arns, Susanne and
                    Palmowski, Karin and Gremse, Felix and Merkle, Ruth and
                    Salopiata, Florian and Klingmüller, Ursula and Jarsch,
                    Michael and Kiessling, Fabian and Lederle, Wiltrud},
  Title           = {Erythropoietin Improves the Accumulation and Therapeutic
                    Effects of Carboplatin by Enhancing Tumor Vascularization
                    and Perfusion},
  JournalTitle    = {Theranostics},
  Date            = {2015},
  DOI             = {10.7150/thno.11304},
  Keywords        = {Lederle-Selection},
  Number          = {8},
  Pages           = {905--918},
  Volume          = {5}
}

@Article{Drescher:716549,
  Author          = {Drescher, Hannah K. and Schippers, Angela and Clahsen,
                    Thomas and Sahin, Hacer and Noels, Heidi and Hornef,
                    Mathias and Wagner, Norbert and Trautwein, Christian and
                    Streetz, Konrad L. and Kroy, Daniela C.},
  Title           = {β 7 -Integrin and {MAdCAM}-1 play opposing roles during
                    the development of non-alcoholic steatohepatitis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/j.jhep.2017.02.001},
  Keywords        = {Schippers-Selection,Wagner-Selection},
  Number          = {6},
  Pages           = {1251--1264},
  Volume          = {66}
}

@Article{Drescher:789112,
  Author          = {Drescher, Hannah K. and Schippers, Angela and Rosenhain,
                    Stefanie and Gremse, Felix and Bongiovanni, Laura and de
                    Bruin, Alain and Eswaran, Sreepradha and Gallage, Suchira
                    U. and Pfister, Dominik and Szydlowska, Marta and
                    Heikenwalder, Mathias and Weiskirchen, Sabine and Wagner,
                    Norbert and Trautwein, Christian and Weiskirchen, Ralf
                    and Kroy, Daniela C.},
  Title           = {L-Selectin/{CD}62L is a Key Driver of Non-Alcoholic
                    Steatohepatitis in Mice and Men},
  JournalTitle    = {Cells},
  Date            = {2020},
  DOI             = {10.3390/cells9051106},
  Keywords        = {,CRC1382-Project B02,CRC1382-Project Q01,CRC1382-Project
                    Q01,CRC1382-Project B02,CRC1382-Project
                    A06,CRC1382-Project A08,CRC1382-Project B02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {5},
  Pages           = {1106},
  Volume          = {9}
}

@Article{Dring:445787,
  Author          = {Döring, Yvonne and Noels, Heidi and Mandl, Manuela and
                    Kramp, Birgit and Neideck, Carlos and Lievens, Dirk and
                    Drechsler, Maik and Megens, Remco T.A. and Tilstam,
                    Pathricia V. and Langer, Marcella and Hartwig, Helene and
                    Theelen, Wendy and Marth, Jamey D. and Sperandio, Markus
                    and Soehnlein, Oliver and Weber, Christian},
  Title           = {Deficiency of the Sialyltransferase {St3Gal4} Reduces
                    Ccl5-Mediated Myeloid Cell Recruitment and Arrest},
  JournalTitle    = {Circ. Res.},
  Date            = {2014},
  DOI             = {10.1161/circresaha.114.302426},
  Number          = {6},
  Pages           = {976--981},
  Subtitle        = {Short Communication},
  Volume          = {114}
}

@Article{Dring:716621,
  Author          = {Döring, Yvonne and Noels, Heidi and van der Vorst,
                    Emiel P.C. and Neideck, Carlos and Egea, Virginia and
                    Drechsler, Maik and Mandl, Manuela and Pawig, Lukas and
                    Jansen, Yvonne and Schröder, Katrin and Bidzhekov, Kiril
                    and Megens, Remco T.A. and Theelen, Wendy and
                    Klinkhammer, Barbara M. and Boor, Peter and Schurgers,
                    Leon and van Gorp, Rick and Ries, Christian and Kusters,
                    Pascal J.H. and van der Wal, Allard and Hackeng, Tilman
                    M. and Gäbel, Gabor and Brandes, Ralf P. and Soehnlein,
                    Oliver and Lutgens, Esther and Vestweber, Dietmar and
                    Teupser, Daniel and Holdt, Lesca M. and Rader, Daniel J.
                    and Saleheen, Danish and Weber, Christian},
  Title           = {Vascular {CXCR4} Limits Atherosclerosis by Maintaining
                    Arterial Integrity},
  JournalTitle    = {Circulation},
  Date            = {2017},
  author+an:default = {1=equal;2=equal},
  Addendum        = equal,
  DOI             = {10.1161/circulationaha.117.027646},
  Keywords        = {Noels-Selection},
  Number          = {4},
  Pages           = {388--403},
  Subtitle        = {Evidence From Mouse and Human Studies},
  Volume          = {136}
}

@Article{Du_Plessis2013-yo,
  Author          = {Du Plessis, Johannie and Vanheel, Hanne and Janssen,
                    Carl E.I. and Roos, Leonie and Slavik, Tomas and
                    Stivaktas, Paraskevi I. and Nieuwoudt, Martin and van
                    Wyk, Stefan G. and Vieira, Warren and Pretorius,
                    Etheresia and Beukes, Mervyn and Farré, Ricard and Tack,
                    Jan and Laleman, Wim and Fevery, Johan and Nevens,
                    Frederik and Roskams, Tania and Van der Merwe, Schalk
                    W.},
  Title           = {Activated intestinal macrophages in patients with
                    cirrhosis release {NO} and {IL}-6 that may disrupt
                    intestinal barrier function},
  JournalTitle    = {J. Hepatol.},
  Date            = {2013},
  DOI             = {10.1016/j.jhep.2013.01.038},
  Number          = {6},
  Pages           = {1125--1132},
  Volume          = {58}
}

@Article{Wang2016-jf,
  Author          = {Wang, Lirui and Fouts, Derrick E. and Stärkel, Peter
                    and Hartmann, Phillipp and Chen, Peng and Llorente,
                    Cristina and DePew, Jessica and Moncera, Kelvin and Ho,
                    Samuel B. and Brenner, David A. and Hooper, Lora V. and
                    Schnabl, Bernd},
  Title           = {Intestinal {REG3} Lectins Protect against Alcoholic
                    Steatohepatitis by Reducing Mucosa-Associated Microbiota
                    and Preventing Bacterial Translocation},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2016},
  DOI             = {10.1016/j.chom.2016.01.003},
  Number          = {2},
  Pages           = {227--239},
  Volume          = {19}
}

@Article{Teltschik2012-jy,
  Author          = {Teltschik, Zora and Wiest, Reiner and Beisner, Julia and
                    Nuding, Sabine and Hofmann, Claudia and Schoelmerich,
                    Juergen and Bevins, Charles L. and Stange, Eduard F. and
                    Wehkamp, Jan},
  Title           = {Intestinal bacterial translocation in rats with
                    cirrhosis is related to compromised paneth cell
                    antimicrobial host defense},
  JournalTitle    = {Hepatology},
  Date            = {2012},
  DOI             = {10.1002/hep.24789},
  Number          = {4},
  Pages           = {1154--1163},
  Volume          = {55}
}

@Article{Duerr2010,
  Author          = {Duerr, C U and Salzman, N H and Dupont, A and Szabo, A
                    and Normark, B H and Normark, S and Locksley, R M and
                    Mellroth, P and Hornef, Mathias W.},
  Title           = {Control of intestinal Nod2-mediated peptidoglycan
                    recognition by epithelium-associated lymphocytes},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2010},
  DOI             = {10.1038/mi.2010.71},
  Number          = {3},
  Pages           = {325--334},
  Volume          = {4}
}

@Article{Dupont:566904,
  Author          = {Dupont, Aline and Kaconis, Yani and Yang, Ines and
                    Albers, Thorben and Woltemate, Sabrina and Heinbockel,
                    Lena and Andersson, Mats and Suerbaum, Sebastian and
                    Brandenburg, Klaus and Hornef, Mathias W},
  Title           = {Intestinal mucus affinity and biological activity of an
                    orally administered antibacterial and anti-inflammatory
                    peptide},
  JournalTitle    = {Gut},
  Date            = {2014},
  DOI             = {10.1136/gutjnl-2014-307150},
  Keywords        = {Hornef-Selection},
  Number          = {2},
  Pages           = {222--232},
  Volume          = {64}
}

@Article{EASL2018-bj,
  Author          = {{European Association for the Study of the Liver}},
  Title           = {{EASL} Clinical Practice Guidelines for the management
                    of patients with decompensated cirrhosis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/j.jhep.2018.03.024},
  Number          = {2},
  Pages           = {406--460},
  Volume          = {69}
}

@Article{Llorente2017-bz,
  Author          = {Llorente, Cristina and Jepsen, Peter and Inamine, Tatsuo
                    and Wang, Lirui and Bluemel, Sena and Wang, Hui J. and
                    Loomba, Rohit and Bajaj, Jasmohan S. and Schubert,
                    Mitchell L. and Sikaroodi, Masoumeh and Gillevet, Patrick
                    M. and Xu, Jun and Kisseleva, Tatiana and Ho, Samuel B.
                    and DePew, Jessica and Du, Xin and Sørensen, Henrik T.
                    and Vilstrup, Hendrik and Nelson, Karen E. and Brenner,
                    David A. and Fouts, Derrick E. and Schnabl, Bernd},
  Title           = {Gastric acid suppression promotes alcoholic liver
                    disease by inducing overgrowth of intestinal
                    Enterococcus},
  JournalTitle    = {Nat. Commun.},
  Date            = {2017},
  DOI             = {10.1038/s41467-017-00796-x},
  Number          = {1},
  Volume          = {8}
}

@Article{Luther2020-bd,
  Author          = {Luther, Jay and Khan, Sanjoy and Gala, Manish K. and
                    Kedrin, Dmitry and Sridharan, Gautham and Goodman,
                    Russell P. and Garber, John J. and Masia, Ricard and
                    Diagacomo, Erik and Adams, Daniel and King, Kevin R. and
                    Piaker, Samuel and Reinecker, Hans-Christian and Yarmush,
                    Martin L. and Argemi, Josepmaria and Bataller, Ramon and
                    Dienstag, Jules L. and Chung, Raymond T. and Patel, Suraj
                    J.},
  Title           = {Hepatic gap junctions amplify alcohol liver injury by
                    propagating {cGAS}-mediated {IRF3} activation},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2020},
  DOI             = {10.1073/pnas.1911870117},
  Number          = {21},
  Pages           = {11667--11673},
  Volume          = {117}
}

@Article{Yang2022-tf,
  Author          = {Yang, Yi and Nguyen, Mytien and Khetrapal, Varnica and
                    Sonnert, Nicole D. and Martin, Anjelica L. and Chen,
                    Haiwei and Kriegel, Martin A. and Palm, Noah W.},
  Title           = {Within-host evolution of a gut pathobiont facilitates
                    liver translocation},
  JournalTitle    = {Nature},
  Date            = {2022},
  DOI             = {10.1038/s41586-022-04949-x},
  Number          = {7919},
  Pages           = {563--570},
  Volume          = {607}
}

@Article{Duan2019-tx,
  Author          = {Duan, Yi and Llorente, Cristina and Lang, Sonja and
                    Brandl, Katharina and Chu, Huikuan and Jiang, Lu and
                    White, Richard C. and Clarke, Thomas H. and Nguyen, Kevin
                    and Torralba, Manolito and Shao, Yan and Liu, Jinyuan and
                    Hernandez-Morales, Adriana and Lessor, Lauren and Rahman,
                    Imran R. and Miyamoto, Yukiko and Ly, Melissa and Gao,
                    Bei and Sun, Weizhong and Kiesel, Roman and Hutmacher,
                    Felix and Lee, Suhan and Ventura-Cots, Meritxell and
                    Bosques-Padilla, Francisco and Verna, Elizabeth C. and
                    Abraldes, Juan G. and Brown, Robert S. and Vargas, Victor
                    and Altamirano, Jose and Caballería, Juan and Shawcross,
                    Debbie L. and Ho, Samuel B. and Louvet, Alexandre and
                    Lucey, Michael R. and Mathurin, Philippe and Garcia-Tsao,
                    Guadalupe and Bataller, Ramon and Tu, Xin M. and Eckmann,
                    Lars and van der Donk, Wilfred A. and Young, Ry and
                    Lawley, Trevor D. and Stärkel, Peter and Pride, David
                    and Fouts, Derrick E. and Schnabl, Bernd},
  Title           = {Bacteriophage targeting of gut bacterium attenuates
                    alcoholic liver disease},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-019-1742-x},
  Number          = {7783},
  Pages           = {505--511},
  Volume          = {575}
}

@Article{Duan2021-iu,
  Author          = {Duan, Yi and Chu, Huikuan and Brandl, Katharina and
                    Jiang, Lu and Zeng, Suling and Meshgin, Nairika and
                    Papachristoforou, Eleni and Argemi, Josepmaria and
                    Mendes, Beatriz G. and Wang, Yanhan and Su, Hua and Sun,
                    Weizhong and Llorente, Cristina and Hendrikx, Tim and
                    Liu, Xiao and Hosseini, Mojgan and Kisseleva, Tatiana and
                    Brenner, David A. and Bataller, Ramon and Ramachandran,
                    Prakash and Karin, Michael and Fu, Wenxian and Schnabl,
                    Bernd},
  Title           = {{CRIg} on liver macrophages clears pathobionts and
                    protects against alcoholic liver disease},
  JournalTitle    = {Nat. Commun.},
  Date            = {2021},
  DOI             = {10.1038/s41467-021-27385-3},
  Number          = {1},
  Pages           = {7172},
  Volume          = {12}
}

@Article{Bruns2012-sj,
  Author          = {Bruns, Tony and Peter, Jack and Reuken, Philipp A. and
                    Grabe, Dominik H. and Schuldes, Sonja R. and Brenmoehl,
                    Julia and Schölmerich, Jürgen and Wiest, Reiner and
                    Stallmach, Andreas},
  Title           = {{NOD2} gene variants are a risk factor for
                    culture-positive spontaneous bacterial peritonitis and
                    monomicrobial bacterascites in cirrhosis},
  JournalTitle    = {Liver Int.},
  Date            = {2011},
  DOI             = {10.1111/j.1478-3231.2011.02561.x},
  Number          = {2},
  Pages           = {223--230},
  Subtitle        = {NOD2 variants and SBP},
  Volume          = {32}
}

@Article{Bruns2012-ln,
  Author          = {Bruns, Tony and Reuken, Philipp A. and Fischer, Janett
                    and Berg, Thomas and Stallmach, Andreas},
  Title           = {Further evidence for the relevance of {TLR2} gene
                    variants in spontaneous bacterial peritonitis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2012},
  DOI             = {10.1016/j.jhep.2011.09.010},
  Number          = {5},
  Pages           = {1207--1208},
  Volume          = {56}
}

@Article{Zeng2016-be,
  Author          = {Zeng, Zhutian and Surewaard, Bas G.J. and Wong, Connie
                    H.Y. and Geoghegan, Joan A. and Jenne, Craig N. and
                    Kubes, Paul},
  Title           = {{CRIg} Functions as a Macrophage Pattern Recognition
                    Receptor to Directly Bind and Capture Blood-Borne
                    Gram-Positive Bacteria},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2016},
  DOI             = {10.1016/j.chom.2016.06.002},
  Number          = {1},
  Pages           = {99--106},
  Volume          = {20}
}

@Article{Bruns2021-af,
  Author          = {Bruns, T. and Trautwein, C.},
  Title           = {Pathogenese und Progression der Leberzirrhose:
                    {Aktuelle} Perspektiven},
  JournalTitle    = {Der Gastroenterologe},
  Date            = {2021},
  DOI             = {10.1007/s11377-021-00517-3},
  Number          = {3},
  Pages           = {137--148},
  Volume          = {16}
}

@Article{Bruns2020-cs,
  Author          = {Bruns, T. and Stallmach, A.},
  Title           = {Gastrointestinale Mikrobiota bei Leberzirrhose:
                    {Pathophysiologische} Veränderungen und therapeutische
                    Interventionen},
  JournalTitle    = {Der Gastroenterologe},
  Date            = {2020},
  DOI             = {10.1007/s11377-020-00436-9},
  Number          = {3},
  Pages           = {194--200},
  Volume          = {15}
}

@Article{Quickert:848650,
  Author          = {Quickert, Stefanie and Würstle, Silvia and Reuken,
                    Philipp A. and Hagel, Stefan and Schneider, Jochen and
                    Schmid, Roland M. and Neugebauer, Sophie and Stallmach,
                    Andreas and Bruns, Tony},
  Title           = {Real-World Effectiveness of Piperacillin/Tazobactam with
                    and without Linezolid for Spontaneous Bacterial
                    Peritonitis},
  JournalTitle    = {Digestive diseases},
  Date            = {2022},
  DOI             = {10.1159/000522259},
  Keywords        = {,CRC1382-Project B07},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)}
}

@Article{EASL2019-fw,
  Author          = {{European Association for the Study of the Liver}},
  Title           = {{EASL} Clinical Practice Guidelines on nutrition in
                    chronic liver disease},
  JournalTitle    = {J. Hepatol.},
  Date            = {2019},
  DOI             = {10.1016/j.jhep.2018.06.024},
  Number          = {1},
  Pages           = {172--193},
  Volume          = {70}
}

@Article{Ebert2014-kt,
  Author          = {Ebert, Birgitta E and Blank, Lars M.},
  Title           = {Successful downsizing for high-throughput {¹³C-MFA}
                    applications},
  JournalTitle    = {Methods Mol. Biol.},
  Date            = {2014},
  DOI             = {10.1007/978-1-4939-1170-7_8},
  Pages           = {127--142},
  Volume          = {1191}
}

@Article{Ebert:217464,
  Author          = {Ebert, Birgitta E. and Lamprecht, Anna-Lena and Steffen,
                    Bernhard and Blank, Lars M.},
  Title           = {Flux-P: {Automating} Metabolic Flux Analysis},
  JournalTitle    = {Metabolites},
  Date            = {2012},
  DOI             = {10.3390/metabo2040872},
  Number          = {4},
  Pages           = {872--890},
  Volume          = {2}
}

@Article{Echle:815758,
  Author          = {Echle, Amelie and Rindtorff, Niklas Timon and Brinker,
                    Titus Josef and Lüdde, Tom and Pearson, Alexander Thomas
                    and Kather, Jakob Nikolas},
  Title           = {Deep learning in cancer pathology: a new generation of
                    clinical biomarkers},
  JournalTitle    = {Br. J. Cancer},
  Date            = {2021},
  DOI             = {10.1038/s41416-020-01122-x},
  Keywords        = {,CRC1382-Project A01},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {686--696},
  Volume          = {124}
}

@Article{Ehling:462134,
  Author          = {Ehling, Josef and Bartneck, Matthias and Wei, Xiao and
                    Gremse, Felix and Fech, Viktor and Möckel, Diana and
                    Baeck, Christer and Hittatiya, Kanishka and Eulberg, Dirk
                    and Luedde, Tom and Kiessling, Fabian and Trautwein,
                    Christian and Lammers, Twan and Tacke, Frank},
  Title           = {{CCL2}-dependent infiltrating macrophages promote
                    angiogenesis in progressive liver fibrosis},
  JournalTitle    = {Gut},
  Date            = {2014},
  DOI             = {10.1136/gutjnl-2013-306294},
  Number          = {12},
  Pages           = {1960--1971},
  Volume          = {63}
}

@Article{El-Serag2012,
  Author          = {El-Serag, Hashem B.},
  Title           = {Epidemiology of Viral Hepatitis and Hepatocellular
                    Carcinoma},
  JournalTitle    = {Gastroenterology},
  Date            = {2012},
  DOI             = {10.1053/j.gastro.2011.12.061},
  Keywords        = {Liver Cancer; Association; Virology; Genetics},
  Number          = {6},
  Pages           = {1264--1273.e1},
  Volume          = {142}
}

@Article{EstvezVzquez:834526,
  Author          = {Estévez-Vázquez, Olga and Benedé-Ubieto, Raquel and
                    Guo, Feifei and Gómez-Santos, Beatriz and Aspichueta,
                    Patricia and Reißing, Johanna and Bruns, Tony and
                    Sanz-García, Carlos and Sydor, Svenja and Bechmann, Lars
                    P. and Maranillo, Eva and Sañudo, José Ramón and
                    Vázquez, María Teresa and Lamas-Paz, Arantza and
                    Morán, Laura and Mazariegos, Marina S. and Ciudin,
                    Andreea and Pericàs, Juan M. and Peligros, María Isabel
                    and Vaquero, Javier and Martínez-Naves, Eduardo and
                    Liedtke, Christian and Regueiro, José R. and Trautwein,
                    Christian and Bañares, Rafael and Cubero, Francisco
                    Javier and Nevzorova, Yulia A.},
  Title           = {Fat},
  JournalTitle    = {Biomedicines},
  Date            = {2021},
  DOI             = {10.3390/biomedicines9101289},
  Keywords        = {,CRC1382-Project B07,CRC1382-Project A02,CRC1382-Project
                    Q03,CRC1382-Project A02,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {10},
  Pages           = {1289},
  Subtitle        = {Quality, or Quantity? What Matters Most for the
                    Progression of Metabolic Associated Fatty Liver Disease
                    ({MAFLD})},
  Volume          = {9}
}

@Article{Fahlenkamp2018-zy,
  Author          = {Fahlenkamp, Ute Lina and Adams, Lisa Christine and
                    Böker, Sarah Maria and Engel, Günther and Huynh Anh,
                    Minh and Wagner, Moritz and Hamm, Bernd and Makowski,
                    Marcus Richard},
  Title           = {Feasibility of gadoxetate disodium enhanced {3D} T1 {MR}
                    cholangiography {(MRC)} with a specific inversion
                    recovery prepulse for the assessment of the hepatobiliary
                    system},
  JournalTitle    = {PLoS One},
  Date            = {2018},
  DOI             = {10.1371/journal.pone.0203476},
  Number          = {9},
  Pages           = {e0203476},
  Volume          = {13}
}

@Article{Eswaran:823132,
  Author          = {Eswaran, Sreepradha and Babbar, Anshu and Drescher,
                    Hannah K. and Hitch, Thomas C. A. and Clavel, Thomas and
                    Muschaweck, Moritz and Ritz, Thomas and Kroy, Daniela C.
                    and Trautwein, Christian and Wagner, Norbert and
                    Schippers, Angela},
  Title           = {Upregulation of Anti-Oxidative Stress Response Improves
                    Metabolic Changes in L-Selectin-Deficient Mice but Does
                    Not Prevent {NAFLD} Progression or Fecal Microbiota
                    Shifts},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2021},
  DOI             = {10.3390/ijms22147314},
  Keywords        = {Wagner-Selection,Schippers-Selection,CRC1382-Project
                    A05,CRC1382-Project Q02,CRC1382-Project
                    B02,CRC1382-Project B02,CRC1382-Project
                    A06,CRC1382-Project A08,CRC1382-Project B02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {14},
  Pages           = {7314},
  Volume          = {22}
}

@Article{Tranah2021-uu,
  Author          = {Tranah, Thomas Henry and Edwards, Lindsey A and Schnabl,
                    Bernd and Shawcross, Debbie Lindsay},
  Title           = {Targeting the gut-liver-immune axis to treat cirrhosis},
  JournalTitle    = {Gut},
  Date            = {2020},
  DOI             = {10.1136/gutjnl-2020-320786},
  Number          = {5},
  Pages           = {982--994},
  Volume          = {70}
}

@Article{Eurich:198327,
  Author          = {Eurich, Dennis and Neumann, Ulf P. and Boas-Knoop,
                    Sabine and Neuhaus, Ruth and Bahra, Marcus and Neuhaus,
                    Peter and Schmitz, Volker},
  Title           = {Transforming Growth Factor-β1-Gene Polymorphism in the
                    Development of Kidney Disease After Liver
                    Transplantation},
  JournalTitle    = {Transplantation},
  Date            = {2012},
  DOI             = {10.1097/tp.0b013e318242be0b},
  Number          = {5},
  Pages           = {555--560},
  Volume          = {93}
}

@Article{Fan2012-uu,
  Author          = {Fan, Biao and Malato, Yann and Calvisi, Diego F and
                    Naqvi, Syed and Razumilava, Nataliya and Ribback, Silvia
                    and Gores, Gregory J and Dombrowski, Frank and Evert,
                    Matthias and Chen, Xin and Willenbring, Holger},
  Title           = {Cholangiocarcinomas can originate from hepatocytes in
                    mice},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2012},
  DOI             = {10.1172/JCI63212},
  Number          = {8},
  Pages           = {2911--2915},
  Volume          = {122}
}

@Article{Feng2021-oz,
  Author          = {Feng, Lixing and Zhang, Wanli and Shen, Qiang and Miao,
                    Chunxiao and Chen, Lijuan and Li, Yiwei and Gu, Xiaofan
                    and Fan, Meng and Ma, Yushui and Wang, Hui and Liu, Xuan
                    and Zhang, Xiongwen},
  Title           = {Bile acid metabolism dysregulation associates with
                    cancer cachexia: {Roles} of liver and gut microbiome},
  JournalTitle    = {J. Cachexia Sarcopenia Muscle},
  Date            = {2021},
  DOI             = {10.1002/jcsm.12798},
  Keywords        = {Bile acids; Cancer cachexia; Gut microbiota; Liver;
                    TUDCA},
  Number          = {6},
  Pages           = {1553--1569},
  Volume          = {12}
}

@Article{Fiegle2019-ij,
  Author          = {Fiegle, E and Doleschel, D and Koletnik, S and Rix, A
                    and Weiskirchen, R and Borkham-Kamphorst, E and
                    Kiessling, F. and Lederle, W.},
  Title           = {Dual {CTLA}-4 and {PD}-L1 Blockade Inhibits Tumor Growth
                    and Liver Metastasis in a Highly Aggressive Orthotopic
                    Mouse Model of Colon Cancer},
  JournalTitle    = {Neoplasia},
  Date            = {2019},
  DOI             = {10.1016/j.neo.2019.07.006},
  Keywords        = {Lederle-Selection},
  Number          = {9},
  Pages           = {932--944},
  Volume          = {21}
}

@Article{Fleige2007,
  Author          = {Fleige, Anne and Alberti, Siegfried and Groöbe, Lothar
                    and Frischmann, Ursula and Geffers, Robert and Muöller,
                    Werner and Nordheim, Alfred and Schippers, Angela},
  Title           = {Serum Response Factor Contributes Selectively to
                    Lymphocyte Development},
  JournalTitle    = {J. Biol. Chem.},
  Date            = {2007},
  DOI             = {10.1074/jbc.m703119200},
  Keywords        = {Schippers-Selection},
  Number          = {33},
  Pages           = {24320--24328},
  Volume          = {282}
}

@Article{Flinders2018-ym,
  Author          = {Flinders, Bryn and Huizing, Lennart R. S. and van
                    Heerden, Marjolein and Cuyckens, Filip and Neumann, Ulf
                    P. and van der Laan, Luc J. W. and Olde Damink, Steven W.
                    M. and Heeren, Ron M. A. and Schaap, Frank G. and
                    Vreeken, Rob J.},
  Title           = {Cross-Species Molecular Imaging of Bile Salts and Lipids
                    in Liver: {Identification} of Molecular Structural
                    Markers in Health and Disease},
  JournalTitle    = {Anal. Chem.},
  Date            = {2018},
  DOI             = {10.1021/acs.analchem.8b01378},
  Keywords        = {Schaap-Selection},
  Number          = {20},
  Pages           = {11835--11846},
  Volume          = {90}
}

@Article{Flint2016,
  Author          = {Flint, Thomas R. and Janowitz, Tobias and Connell,
                    Claire M. and Roberts, Edward W. and Denton, Alice E. and
                    Coll, Anthony P. and Jodrell, Duncan I. and Fearon,
                    Douglas T.},
  Title           = {Tumor-Induced {IL}-6 Reprograms Host Metabolism to
                    Suppress Anti-tumor Immunity},
  JournalTitle    = {Cell Metab.lism},
  Date            = {2016},
  DOI             = {10.1016/j.cmet.2016.10.010},
  Number          = {5},
  Pages           = {672--684},
  Volume          = {24}
}

@Article{Forand2016-tx,
  Author          = {Forand, Anne and Koumakis, Eugénie and Rousseau, Alice
                    and Sassier, Yohann and Journe, Clément and Merlin,
                    Jean-François and Leroy, Christine and Boitez, Valérie
                    and Codogno, Patrice and Friedlander, Gérard and Cohen,
                    Isabelle},
  Title           = {Disruption of the phosphate transporter Pit1 in
                    hepatocytes improves glucose metabolism and insulin
                    signaling by modulating the {USP7/IRS1} interaction},
  JournalTitle    = {Cell Rep.},
  Date            = {2016},
  DOI             = {10.1016/j.celrep.2016.08.012},
  Number          = {10},
  Pages           = {2736--2748},
  Volume          = {16}
}

@Article{Ford2014,
  Author          = {Ford, Laura B. and Cerovic, Vuk and Milling, Simon W. F.
                    and Graham, Gerard J. and Hansell, Chris A. H. and Nibbs,
                    Robert J. B.},
  Title           = {Characterization of Conventional and Atypical Receptors
                    for the Chemokine {CCL2} on Mouse Leukocytes},
  JournalTitle    = {J. Immunol.},
  Date            = {2014},
  DOI             = {10.4049/jimmunol.1303236},
  Keywords        = {Cerovic-Selection},
  Number          = {1},
  Pages           = {400--411},
  Volume          = {193}
}

@Article{Freimuth:238220,
  Author          = {Freimuth, Julia and Bangen, Jörg-Martin and Lambertz,
                    Daniela and Hu, Wei and Nevzorova, Yulia Alexandrowna and
                    Sonntag, Roland and Gassler, Nikolaus and Riethmacher,
                    Dieter and Trautwein, Christian and Liedtke, Christian},
  Title           = {Loss of caspase-8 in hepatocytes accelerates the onset
                    of liver regeneration in mice through premature nuclear
                    factor kappa B activation},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26538},
  Keywords        = {Liedtke-Selection},
  Number          = {5},
  Pages           = {1779--1789},
  Subtitle        = {Freimuth, Bangen, et al.},
  Volume          = {58}
}

@Article{Friedrich2013-ko,
  Author          = {Friedrich, Kilian and Rupp, Christian and Hov, Johannes
                    Roksund and Steinebrunner, Niels and Weiss, Karl-Heinz
                    and Stiehl, Adolf and Brune, Maik and Schaefer, Petra
                    Kloeters Yvonne and Schemmer, Peter and Sauer, Peter and
                    Schirmacher, Peter and Runz, Heiko and Karlsen, Tom
                    Hemming and Stremmel, Wolfgang and Gotthardt, Daniel
                    Nils},
  Title           = {A Frequent {PNPLA3} Variant Is a Sex Specific Disease
                    Modifier in {PSC} Patients with Bile Duct Stenosis},
  JournalTitle    = {PLoS One},
  Date            = {2013},
  DOI             = {10.1371/journal.pone.0058734},
  Number          = {3},
  Pages           = {e58734},
  Volume          = {8}
}

@Article{Fries:848142,
  Author          = {Fries, Charlotte M. and Haange, Sven-Bastiaan and
                    Rolle-Kampczyk, Ulrike and Till, Andreas and Lammert,
                    Mathis and Grasser, Linda and Medawar, Evelyn and
                    Dietrich, Arne and Horstmann, Annette and von Bergen,
                    Martin and Fenske, Wiebke K.},
  Title           = {Metabolic Profile and Metabolite Analyses in Extreme
                    Weight Responders to Gastric Bypass Surgery},
  JournalTitle    = {Metabolites},
  Date            = {2022},
  DOI             = {10.3390/metabo12050417},
  Keywords        = {,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {5},
  Pages           = {417},
  Volume          = {12}
}

@Article{Frissen2021-xp,
  Author          = {Frissen, Mick and Liao, Lijun and Schneider, Kai Markus
                    and Djudjaj, Sonja and Haybaeck, Johannes and Wree,
                    Alexander and Rolle-Kampczyk, Ulrike and von Bergen,
                    Martin and Latz, Eicke and Boor, Peter and Trautwein,
                    Christian},
  Title           = {Bidirectional role of {NLRP3} during acute and chronic
                    cholestatic liver injury},
  JournalTitle    = {Hepatology},
  Date            = {2021},
  DOI             = {10.1002/hep.31494},
  Keywords        = {Trautwein-Selection},
  Number          = {5},
  Pages           = {1836--1854},
  Volume          = {73}
}

@Article{Fromme415,
  Author          = {Fromme, Malin and Schneider, Carolin V. and Pereira,
                    Vitor and Hamesch, Karim and Pons, Monica and Reichert,
                    Matthias C and Benini, Federica and Ellis, Paul and H
                    Thorhauge, Katrine and Mandorfer, Mattias and Burbaum,
                    Barbara and Woditsch, Vivien and Chorostowska-Wynimko,
                    Joanna and Verbeek, Jef and Nevens, Frederik and Genesca,
                    Joan and Miravitlles, Marc and Nuñez, Alexa and
                    Schaefer, Benedikt and Zoller, Heinz and Janciauskiene,
                    Sabina and Abreu, Nélia and Jasmins, Luís and Gaspar,
                    Rui and Liberal, Rodrigo and Macedo, Guilherme and
                    Mahadeva, Ravi and Gomes, Catarina and Schneider, Kai
                    Markus and Trauner, Michael and Krag, Aleksander and
                    Gooptu, Bibek and Thorburn, Douglas and Marshall, Aileen
                    and Hurst, John R and Lomas, David A and Lammert, Frank
                    and Gaisa, Nadine T and Clark, Virginia and Griffiths,
                    William and Trautwein, Christian and Turner, Alice M and
                    McElvaney, Noel G and Strnad, Pavel},
  Title           = {Hepatobiliary phenotypes of adults with alpha-1
                    antitrypsin deficiency},
  Addendum        = equalpreliminarywork,
  JournalTitle    = {Gut},
  Date            = {2021},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1136/gutjnl-2020-323729},
  EPrint          = {https://gut.bmj.com/content/71/2/415.full.pdf},
  Keywords        = {SchneiderCV-Selection,Strnad-Selection},
  Number          = {2},
  Pages           = {415--423},
  Volume          = {71}
}

@Article{Fuchs2022-uc,
  Author          = {Fuchs, Claudia D and Trauner, Michael},
  Title           = {Role of bile acids and their receptors in
                    gastrointestinal and hepatic pathophysiology},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2022},
  DOI             = {10.1038/s41575-021-00566-7},
  Number          = {7},
  Pages           = {432--450},
  Volume          = {19}
}

@Article{Luciani2022-pl,
  Author          = {Luciani, Cécilia and Hager, Fabian Tobias and Cerovic,
                    Vuk and Lelouard, Hugues},
  Title           = {Dendritic cell functions in the inductive and effector
                    sites of intestinal immunity},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2021},
  DOI             = {10.1038/s41385-021-00448-w},
  Number          = {1},
  Pages           = {40--50},
  Volume          = {15}
}

@Article{Fulde:756780,
  Author          = {Fulde, Marcus and Sommer, Felix and Chassaing, Benoit
                    and van Vorst, Kira and Dupont, Aline and Hensel, Michael
                    and Basic, Marijana and Klopfleisch, Robert and
                    Rosenstiel, Philip and Bleich, André and Bäckhed,
                    Fredrik and Gewirtz, Andrew T. and Hornef, Mathias W.},
  Title           = {Neonatal selection by Toll-like receptor 5 influences
                    long-term gut microbiota composition},
  JournalTitle    = {Nature},
  Date            = {2018},
  DOI             = {10.1038/s41586-018-0395-5},
  Keywords        = {Hornef-Selection},
  Number          = {7719},
  Pages           = {489--493},
  Volume          = {560}
}

@Article{Fulde:828376,
  Author          = {Fulde, Marcus and van Vorst, Kira and Zhang, Kaiyi and
                    Westermann, Alexander J. and Busche, Tobias and Huei,
                    Yong Chiun and Welitschanski, Katharina and Froh, Isabell
                    and Pägelow, Dennis and Plendl, Johanna and Pfarrer,
                    Christiane and Kalinowski, Jörn and Vogel, Jörg and
                    Valentin-Weigand, Peter and Hensel, Michael and Tedin,
                    Karsten and Repnik, Urska and Hornef, Mathias W.},
  Title           = {{SPI}2 T3{SS} effectors facilitate enterocyte apical to
                    basolateral transmigration of Salmonella-containing
                    vacuoles in vivo},
  JournalTitle    = {Gut microbes},
  Date            = {2021},
  DOI             = {10.1080/19490976.2021.1973836},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {1973836},
  Volume          = {13}
}

@Article{Gadaleta2011-qf,
  Author          = {Gadaleta, Raffaella M and Oldenburg, Bas and Willemsen,
                    Ellen C L and Spit, Maureen and Murzilli, Stefania and
                    Salvatore, Lorena and Klomp, Leo W J and Siersema, Peter
                    D and van Erpecum, Karel J and van Mil, Saskia W C},
  Title           = {Activation of bile salt nuclear receptor {FXR} is
                    repressed by pro-inflammatory cytokines activating
                    {NF-$\kappa$B} signaling in the intestine},
  JournalTitle    = {Biochim. Biophys. Acta},
  Date            = {2011},
  DOI             = {10.1016/j.bbadis.2011.04.005},
  Number          = {8},
  Pages           = {851--858},
  Volume          = {1812}
}

@Article{Gajjala2019-iy,
  Author          = {Gajjala, Prathibha R and Bruck, Heike and Noels, Heidi
                    and Heinze, Georg and Ceccarelli, Francesco and Kribben,
                    Andreas and Saez-Rodriguez, Julio and Marx, Nikolaus and
                    Zidek, Walter and Jankowski, Joachim and Jankowski,
                    Vera},
  Title           = {Novel plasma peptide markers involved in the pathology
                    of {CKD} identified using mass spectrometric approach},
  JournalTitle    = {J. Mol. Med.},
  Date            = {2019},
  DOI             = {10.1007/s00109-019-01823-8},
  Keywords        = {Chronic kidney disease; Disease progression; End-stage
                    renal disease; Systems medicine; peptidomics;
                    proteomics},
  Number          = {10},
  Pages           = {1451--1463},
  Volume          = {97}
}

@Article{Galvez2017-rx,
  Author          = {Gálvez, Eric J C and Iljazovic, Aida and Gronow, Achim
                    and Flavell, Richard and Strowig, Till},
  Title           = {Shaping of intestinal Microbiota in Nlrp6- and
                    Rag2-deficient mice depends on community structure},
  JournalTitle    = {Cell Rep.},
  Date            = {2017},
  DOI             = {10.1016/j.celrep.2017.12.027},
  Keywords        = {Nlrp6; adaptive immunity; familial transmission; gut
                    biogeography; host-microbiota interaction; intestinal
                    microbiota},
  Number          = {13},
  Pages           = {3914--3926},
  Volume          = {21}
}

@Article{GanalVonarburg:793457,
  Author          = {Ganal-Vonarburg, Stephanie C. and Hornef, Mathias W. and
                    Macpherson, Andrew J.},
  Title           = {Microbial-host molecular exchange and its functional
                    consequences in early mammalian life},
  JournalTitle    = {Science / Science now},
  Date            = {2020},
  DOI             = {10.1126/science.aba0478},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {6491},
  Pages           = {604--607},
  Volume          = {368}
}

@Article{Gao2021-wj,
  Author          = {Gao, Rachel Y and Shearn, Colin T and Orlicky, David J
                    and Battista, Kayla D and Alexeev, Erica E and
                    Cartwright, Ian M and Lanis, Jordi M and Kostelecky,
                    Rachael E and Ju, Cynthia and Colgan, Sean P and
                    Fennimore, Blair P},
  Title           = {Bile acids modulate colonic {MAdCAM-1} expression in a
                    murine model of combined cholestasis and colitis},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2021},
  DOI             = {10.1038/s41385-020-00347-6},
  Number          = {2},
  Pages           = {479--490},
  Volume          = {14}
}

@Article{Gautheron:446083,
  Author          = {Gautheron, Jérémie and Vucur, Mihael and Reisinger,
                    Florian and Cardenas, David Vargas and Roderburg,
                    Christoph and Koppe, Christiane and Kreggenwinkel, Karina
                    and Schneider, Anne Theres and Bartneck, Matthias and
                    Neumann, Ulf Peter and Canbay, Ali and Reeves, Helen
                    Louise and Luedde, Mark and Tacke, Frank and Trautwein,
                    Christian and Heikenwalder, Mathias and Luedde, Tom},
  Title           = {A positive feedback loop between {RIP} 3 and {JNK}
                    controls non‐alcoholic steatohepatitis},
  JournalTitle    = {EMBO Mol. Med.},
  Date            = {2014},
  DOI             = {10.15252/emmm.201403856},
  Keywords        = {Lüdde-Selection},
  Number          = {8},
  Pages           = {1062--1074},
  Volume          = {6}
}

@Article{Gautheron:683068,
  Author          = {Gautheron, Jérémie and Vucur, Mihael and Schneider,
                    Anne T. and Severi, Ilenia and Roderburg, Christoph and
                    Roy, Sanchari and Bartneck, Matthias and Schrammen, Peter
                    and Diaz, Mauricio Berriel and Ehling, Josef and Gremse,
                    Felix and Heymann, Felix and Koppe, Christiane and
                    Lammers, Twan and Kiessling, Fabian and Van Best, Niels
                    and Pabst, Oliver and Courtois, Gilles and Linkermann,
                    Andreas and Krautwald, Stefan and Neumann, Ulf P. and
                    Tacke, Frank and Trautwein, Christian and Green, Douglas
                    R. and Longerich, Thomas and Frey, Norbert and Luedde,
                    Mark and Bluher, Matthias and Herzig, Stephan and
                    Heikenwalder, Mathias and Luedde, Tom},
  Title           = {The necroptosis-inducing kinase {RIPK3} dampens adipose
                    tissue inflammation and glucose intolerance},
  JournalTitle    = {Nat. Commun.},
  Date            = {2016},
  DOI             = {10.1038/ncomms11869},
  ids             = {gautheron2016a},
  Keywords        = {Lüdde-Selection},
  Number          = {1},
  Pages           = {11869},
  Volume          = {7}
}

@Article{Germer2020-lz,
  Author          = {Germer, Andrea and Tiso, Till and Müller, Conrad and
                    Behrens, Beate and Vosse, Christian and Scholz, Karen and
                    Froning, Matti and Hayen, Heiko and Blank, Lars M.},
  Title           = {Exploiting the natural diversity of {RhlA}
                    acyltransferases for the synthesis of the rhamnolipid
                    precursor 3-(3-hydroxyalkanoyloxy)alkanoic acid},
  JournalTitle    = {Appl. Environ. Microbiol.},
  Date            = {2020},
  DOI             = {10.1128/AEM.02317-19},
  Number          = {6},
  Volume          = {86}
}

@Article{Ghallab2022-tr,
  Author          = {Ghallab, Ahmed and Hassan, Reham and Hofmann, Ute and
                    Friebel, Adrian and Hobloss, Zaynab and Brackhagen, Lisa
                    and Begher-Tibbe, Brigitte and Myllys, Maiju and
                    Reinders, Joerg and Overbeck, Nina and Sezgin, Selahaddin
                    and Zühlke, Sebastian and Seddek, Abdel-latif and Murad,
                    Walaa and Brecklinghaus, Tim and Kappenberg, Franziska
                    and Rahnenführer, Jörg and González, Daniela and
                    Goldring, Christopher and Copple, Ian M. and Marchan,
                    Rosemarie and Longerich, Thomas and Vucur, Mihael and
                    Luedde, Tom and Urban, Stephan and Canbay, Ali and
                    Schreiter, Thomas and Trauner, Michael and Akakpo, Jephte
                    Y. and Olyaee, Mojtaba and Curry, Steven C. and Sowa,
                    Jan-Peter and Jaeschke, Hartmut and Hoehme, Stefan and
                    Hengstler, Jan G.},
  Title           = {Interruption of bile acid uptake by hepatocytes after
                    acetaminophen overdose ameliorates hepatotoxicity},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2022.01.020},
  Number          = {1},
  Pages           = {71--83},
  Volume          = {77}
}

@Article{Ghimire2020,
  Author          = {Ghimire, Laxman and Paudel, Sagar and Jin, Liliang and
                    Jeyaseelan, Samithamby},
  Title           = {The {NLRP6} inflammasome in health and disease},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2020},
  DOI             = {10.1038/s41385-020-0256-z},
  Keywords        = {Animals; Cell Communication; Cell
                    Transformation,Neoplastic/genetics/metabolism; *Disease
                    Susceptibility; Gastrointestinal Microbiome;
                    *Homeostasis; Host-Pathogen
                    Interactions/genetics/immunology; Humans;
                    Inflammasomes/*metabolism;
                    Inflammation/etiology/metabolism; Intestinal
                    Mucosa/immunology/metabolism/microbiology; Intracellular
                    Signaling Peptides and Proteins/*metabolism; Metabolic
                    Diseases/etiology/metabolism; Signal Transduction},
  Note            = {PMC7493825},
  Number          = {3},
  Pages           = {388--398},
  Volume          = {13}
}

@Article{Gillies2016-ib,
  Author          = {Gillies, Robert J. and Kinahan, Paul E. and Hricak,
                    Hedvig},
  Title           = {Radiomics: {Images} Are More than Pictures, They Are
                    Data},
  JournalTitle    = {Radiology},
  Date            = {2016},
  DOI             = {10.1148/radiol.2015151169},
  Number          = {2},
  Pages           = {563--577},
  Volume          = {278}
}

@Article{Han2021-eo,
  Author          = {Han, Tianyu and Kather, Jakob Nikolas and Pedersoli,
                    Federico and Zimmermann, Markus and Keil, Sebastian and
                    Schulze-Hagen, Maximilian and Terwoelbeck, Marc and
                    Isfort, Peter and Haarburger, Christoph and Kiessling,
                    Fabian and Schulz, Volkmar and Kuhl, Christiane and
                    Nebelung, Sven and Truhn, Daniel},
  Title           = {Image prediction of disease progression by style-based
                    manifold extrapolation},
  JournalTitle    = {arXiv},
  Date            = {2021},
  DOI             = {10.48550/arXiv.2111.11439}
}

@Article{Han2020-up,
  Author          = {Han, Tianyu and Nebelung, Sven and Haarburger, Christoph
                    and Horst, Nicolas and Reinartz, Sebastian and Merhof,
                    Dorit and Kiessling, Fabian and Schulz, Volkmar and
                    Truhn, Daniel},
  Title           = {Breaking medical data sharing boundaries by using
                    synthesized radiographs},
  JournalTitle    = {Sci. Adv.},
  Date            = {2020},
  DOI             = {10.1126/sciadv.abb7973},
  Number          = {49},
  Pages           = {eabb7973},
  Volume          = {6}
}

@Article{Han2021-de,
  Author          = {Han, Tianyu and Nebelung, Sven and Pedersoli, Federico
                    and Zimmermann, Markus and Schulze-Hagen, Maximilian and
                    Ho, Michael and Haarburger, Christoph and Kiessling,
                    Fabian and Kuhl, Christiane and Schulz, Volkmar and
                    Truhn, Daniel},
  Title           = {Advancing diagnostic performance and clinical usability
                    of neural networks via adversarial training and dual
                    batch normalization},
  JournalTitle    = {Nat. Commun.},
  Date            = {2021},
  DOI             = {10.1038/s41467-021-24464-3},
  Number          = {1},
  Pages           = {4315},
  Volume          = {12}
}

@Article{Ginhoux2016-my,
  Author          = {Ginhoux, Florent and Schultze, Joachim L and Murray,
                    Peter J and Ochando, Jordi and Biswas, Subhra K},
  Title           = {New insights into the multidimensional concept of
                    macrophage ontogeny, activation and function},
  JournalTitle    = {Nat. Immunol.},
  Date            = {2016},
  DOI             = {10.1038/ni.3324},
  Number          = {1},
  Pages           = {34--40},
  Volume          = {17}
}

@Article{Gldiken:572510,
  Author          = {Guldiken, Nurdan and Zhou, Qin and Kucukoglu, Ozlem and
                    Rehm, Melanie and Levada, Kateryna and Gross, Annika and
                    Kwan, Raymond and James, Laura P. and Trautwein,
                    Christian and Omary, M. Bishr and Strnad, Pavel},
  Title           = {Human keratin 8 variants promote mouse acetaminophen
                    hepatotoxicity coupled with c-jun amino-terminal kinase
                    activation and protein adduct formation},
  JournalTitle    = {Hepatology},
  Date            = {2015},
  DOI             = {10.1002/hep.27891},
  ids             = {guldiken2015b},
  Keywords        = {Guldiken-Selection},
  Number          = {3},
  Pages           = {876--886},
  Volume          = {62}
}

@Article{Gldiken:685023,
  Author          = {Guldiken, Nurdan and Kobazi Ensari, Gokce and Lahiri,
                    Pooja and Couchy, Gabrielle and Preisinger, Christian and
                    Liedtke, Christian and Zimmermann, Henning W. and Ziol,
                    Marianne and Boor, Peter and Zucman-Rossi, Jessica and
                    Trautwein, Christian and Strnad, Pavel},
  Title           = {Keratin 23 is a stress-inducible marker of mouse and
                    human ductular reaction in liver disease},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2016.04.024},
  ids             = {guldiken2016a},
  Keywords        = {Guldiken-Selection,Strnad-Selection},
  Number          = {3},
  Pages           = {552--559},
  Volume          = {65}
}

@Article{Gldiken:719952,
  Author          = {Guldiken, N. and Zhou, Q. and Kucukoglu, O. and Rehm, M.
                    and Levada, K. and James, L.P. and Trautwein, C. and
                    Bishr Omary, M. and Strnad, P.},
  Title           = {P1113 : {Human} Keratin 8 variants promote mouse
                    acetaminophen hepatotoxicity coupled with {JNK}
                    activation and protein adduct formation},
  JournalTitle    = {J. Hepatol.},
  Date            = {2015},
  DOI             = {10.1016/s0168-8278(15)31310-6},
  Number          = {Supplement 2},
  Organization    = {International Liver Congress™ 2015 - 50th Annual
                    meeting of the European Association for the Study of the
                    Liver, Vienna (Austria), 22 Apr 2015 - 26 Apr 2015},
  Pages           = {S767--S768},
  Volume          = {62}
}

@Article{Gola2021-ur,
  Author          = {Gola, Anita and Dorrington, Michael G. and Speranza,
                    Emily and Sala, Claudia and Shih, Rochelle M. and Radtke,
                    Andrea J. and Wong, Harikesh S. and Baptista, Antonio P.
                    and Hernandez, Jonathan M. and Castellani, Gastone and
                    Fraser, Iain D. C. and Germain, Ronald N.},
  Title           = {Commensal-driven immune zonation of the liver promotes
                    host defence},
  JournalTitle    = {Nature},
  Date            = {2020},
  DOI             = {10.1038/s41586-020-2977-2},
  Number          = {7840},
  Pages           = {131--136},
  Volume          = {589}
}

@Article{GomezdeAguero2016,
  Author          = {Gomez de Agüero, Mercedes and Ganal-Vonarburg,
                    Stephanie C. and Fuhrer, Tobias and Rupp, Sandra and
                    Uchimura, Yasuhiro and Li, Hai and Steinert, Anna and
                    Heikenwalder, Mathias and Hapfelmeier, Siegfried and
                    Sauer, Uwe and McCoy, Kathy D. and Macpherson, Andrew
                    J.},
  Title           = {The maternal microbiota drives early postnatal innate
                    immune development},
  JournalTitle    = {Science},
  Date            = {2016},
  DOI             = {10.1126/science.aad2571},
  ids             = {Gomez_de_Aguero2016-yw},
  Number          = {6279},
  Pages           = {1296--1302},
  Volume          = {351}
}

@Article{Gori2020-vv,
  Author          = {Gori, Manuele and Altomare, Annamaria and Cocca, Silvia
                    and Solida, Eleonora and Ribolsi, Mentore and Carotti,
                    Simone and Rainer, Alberto and Francesconi, Maria and
                    Morini, Sergio and Cicala, Michele and Guarino, Michele
                    Pier Luca},
  Title           = {Palmitic acid affects intestinal epithelial barrier
                    integrity and permeability in vitro},
  JournalTitle    = {Antioxidants (Basel)},
  Date            = {2020},
  DOI             = {10.3390/antiox9050417},
  Keywords        = {Caco-2 monolayer; adherens junctions.; gut barrier
                    integrity; intestinal permeability; palmitic acid; tight
                    junctions},
  Number          = {5},
  Pages           = {417},
  Volume          = {9}
}

@Article{Plitas2016,
  Author          = {Plitas, George and Konopacki, Catherine and Wu, Kenmin
                    and Bos, Paula D. and Morrow, Monica and Putintseva,
                    Ekaterina V. and Chudakov, Dmitriy M. and Rudensky,
                    Alexander Y.},
  Title           = {Regulatory T Cells Exhibit Distinct Features in Human
                    Breast Cancer},
  JournalTitle    = {Immunity},
  Date            = {2016},
  DOI             = {10.1016/j.immuni.2016.10.032},
  Number          = {5},
  Pages           = {1122--1134},
  Volume          = {45}
}

@Article{Graffmann2016-jv,
  Author          = {Graffmann, Nina and Ring, Sarah and Kawala, Marie-Ann
                    and Wruck, Wasco and Ncube, Audrey and Trompeter,
                    Hans-Ingo and Adjaye, James},
  Title           = {Modeling Nonalcoholic Fatty Liver Disease with Human
                    Pluripotent Stem Cell-Derived Immature Hepatocyte-Like
                    Cells Reveals Activation of {PLIN2} and Confirms
                    Regulatory Functions of Peroxisome Proliferator-Activated
                    Receptor Alpha},
  JournalTitle    = {Stem Cells Dev.},
  Date            = {2016},
  DOI             = {10.1089/scd.2015.0383},
  Number          = {15},
  Pages           = {1119--1133},
  Volume          = {25}
}

@Article{Bajer2017-qk,
  Author          = {Bajer, Lukas and Kverka, Miloslav and Kostovcik, Martin
                    and Macinga, Peter and Dvorak, Jiri and Stehlikova,
                    Zuzana and Brezina, Jan and Wohl, Pavel and Spicak,
                    Julius and Drastich, Pavel},
  Title           = {Distinct gut microbiota profiles in patients with
                    primary sclerosing cholangitis and ulcerative colitis},
  JournalTitle    = {World J. Gastroenterol.},
  Date            = {2017},
  DOI             = {10.3748/wjg.v23.i25.4548},
  Number          = {25},
  Pages           = {4548},
  Volume          = {23}
}

@Article{Grace2013,
  Author          = {Grace, Josephine A. and Klein, Sabine and Herath,
                    Chandana B. and Granzow, Michaela and Schierwagen, Robert
                    and Masing, Noemi and Walther, Thomas and Sauerbruch,
                    Tilman and Burrell, Louise M. and Angus, Peter W. and
                    Trebicka, Jonel},
  Title           = {Activation of the Mas Receptor by Angiotensin-(1–7) in
                    the {Renin–Angiotensin} System Mediates Mesenteric
                    Vasodilatation in Cirrhosis},
  JournalTitle    = {Gastroenterology},
  Date            = {2013},
  DOI             = {10.1053/j.gastro.2013.06.036},
  Number          = {4},
  Pages           = {874--884.e5},
  Volume          = {145}
}

@Article{Graham2021-ef,
  Author          = {Graham, Jonathon J. and Mukherjee, Sujit and Yuksel,
                    Muhammad and Mateos, Rebeca Sanabria and Si, Tengfei and
                    Huang, Zhenlin and Huang, Xiahong and Arqoub, Hadil Abu
                    and Patel, Vishal and McPhail, Mark and Zen, Yoh and
                    Heaton, Nigel and Longhi, Maria Serena and Heneghan,
                    Michael A. and Liberal, Rodrigo and Vergani, Diego and
                    Mieli-Vergani, Giorgina and Ma, Yun and Hayee,
                    Bu'Hussain},
  Title           = {Aberrant hepatic trafficking of gut-derived T cells is
                    not specific to primary sclerosing cholangitis},
  JournalTitle    = {Hepatology},
  Date            = {2021},
  DOI             = {10.1002/hep.32193},
  Number          = {3},
  Pages           = {518--530},
  Volume          = {75}
}

@Article{Granzow2014,
  Author          = {Granzow, Michaela and Schierwagen, Robert and Klein,
                    Sabine and Kowallick, Benita and Huss, Sebastian and
                    Linhart, Markus and Mazar, Irela G. Reza and Görtzen,
                    Jan and Vogt, Annabelle and Schildberg, Frank A. and
                    Gonzalez-Carmona, Maria A. and Wojtalla, Alexandra and
                    Krämer, Benjamin and Nattermann, Jacob and Siegmund,
                    Sören V. and Werner, Nikos and Fürst, Dieter O. and
                    Laleman, Wim and Knolle, Percy and Shah, Vijay H. and
                    Sauerbruch, Tilman and Trebicka, Jonel},
  Title           = {Angiotensin-{II} type 1 receptor-mediated {Janus} kinase
                    2 activation induces liver fibrosis},
  JournalTitle    = {Hepatology},
  Date            = {2014},
  DOI             = {10.1002/hep.27117},
  Number          = {1},
  Pages           = {334--348},
  Volume          = {60}
}

@Article{Gremse:158778,
  Author          = {Gremse, Felix and Grouls, Christoph and Palmowski,
                    Moritz and Lammers, Twan and de Vries, Anke and Grüll,
                    Holger and Das, Marco and Mühlenbruch, Georg and Akhtar,
                    Shamima and Schober, Andreas and Kiessling, Fabian},
  Title           = {Virtual Elastic Sphere Processing Enables Reproducible
                    Quantification of Vessel Stenosis at {CT} and {MR}
                    Angiography},
  JournalTitle    = {Radiology},
  Date            = {2011},
  DOI             = {10.1148/radiol.11110069},
  Keywords        = {Kießling-Selection},
  Number          = {3},
  Pages           = {709--717},
  Volume          = {260}
}

@Article{Yang2022,
  Author          = {Yang, Chao and Jin, Jingsi and Yang, Yuanqin and Sun,
                    Hongxiang and Wu, Lingling and Shen, Mingyi and Hong,
                    Xiaochuan and Li, Wenwen and Lu, Lu and Cao, Dongqing and
                    Wang, Xinran and Sun, Jing and Ye, Youqiong and Su, Bing
                    and Deng, Liufu},
  Title           = {Androgen receptor-mediated {CD}8+ T cell stemness
                    programs drive sex differences in antitumor immunity},
  JournalTitle    = {Immunity},
  Date            = {2022},
  DOI             = {10.1016/j.immuni.2022.05.012},
  Number          = {7},
  Pages           = {1268--1283.e9},
  Volume          = {55}
}

@Article{Ray2020,
  Author          = {Ray, Anita L. and Nofchissey, Robert A. and Khan, Maaz
                    A. and Reidy, Megan A. and Lerner, Megan R. and Wu,
                    Xiangyan and Guo, Shaoxuan and Hill, Spencer L. and
                    Weygant, Nathaniel and Adams, Sarah F. and Castillo,
                    Eliseo F. and Berry, William L. and Stout, Michael B. and
                    Morris, Katherine T.},
  Title           = {The role of sex in the innate and adaptive immune
                    environment of metastatic colorectal cancer},
  JournalTitle    = {Br. J. Cancer},
  Date            = {2020},
  DOI             = {10.1038/s41416-020-0913-8},
  Number          = {4},
  Pages           = {624--632},
  Volume          = {123}
}

@Article{Theek2018-fv,
  Author          = {Theek, Benjamin and Opacic, Tatjana and Magnuska,
                    Zuzanna and Lammers, Twan and Kiessling, Fabian},
  Title           = {Radiomic analysis of contrast-enhanced ultrasound data},
  JournalTitle    = {Sci. Rep.},
  Date            = {2018},
  DOI             = {10.1038/s41598-018-29653-7},
  Number          = {1},
  Pages           = {11359},
  Volume          = {8}
}

@Article{Gremse:445387,
  Author          = {Gremse, Felix and Theek, Benjamin and Kunjachan, Sijumon
                    and Lederle, Wiltrud and Pardo, Alessa and Barth, Stefan
                    and Lammers, Twan and Naumann, Uwe and Kiessling,
                    Fabian},
  Title           = {Absorption Reconstruction Improves Biodistribution
                    Assessment of Fluorescent Nanoprobes Using Hybrid
                    Fluorescence-mediated Tomography},
  JournalTitle    = {Theranostics},
  Date            = {2014},
  DOI             = {10.7150/thno.9293},
  Keywords        = {Gremse-Selection},
  Number          = {10},
  Pages           = {960--971},
  Volume          = {4}
}

@Article{Gremse:480932,
  Author          = {Gremse, Felix and Höfter, Andreas and Schwen, Lars Ole
                    and Kiessling, Fabian and Naumann, Uwe},
  Title           = {{GPU}-Accelerated Sparse Matrix-Matrix Multiplication by
                    Iterative Row Merging},
  JournalTitle    = {SIAM J. Sci. Comput.},
  Date            = {2015},
  DOI             = {10.1137/130948811},
  Keywords        = {Gremse-Selection},
  Number          = {1},
  Pages           = {C54--C71},
  Volume          = {37}
}

@Article{Gremse:571274,
  Author          = {Gremse, Felix and Doleschel, Dennis and Zafarnia, Sara
                    and Babler, Anne and Jahnen-Dechent, Willi and Lammers,
                    Twan and Lederle, Wiltrud and Kiessling, Fabian},
  Title           = {Hybrid {µCT}-{FMT} imaging and image analysis},
  JournalTitle    = {J. Vis. Exp.},
  Date            = {2015},
  DOI             = {10.3791/52770},
  Keywords        = {Gremse-Selection},
  Number          = {100},
  Pages           = {e52770}
}

@Article{Gremse:667943,
  Author          = {Gremse, Felix and Höfter, Andreas and Razik, Lukas and
                    Kiessling, Fabian and Naumann, Uwe},
  Title           = {{GPU}-accelerated adjoint algorithmic differentiation},
  JournalTitle    = {Comput. Phys. Commun.},
  Date            = {2016},
  DOI             = {10.1016/j.cpc.2015.10.027},
  Keywords        = {Gremse-Selection},
  Pages           = {300--311},
  Volume          = {200}
}

@Article{Gremse:685222,
  Author          = {Gremse, Felix and Stärk, Marius and Ehling, Josef and
                    Menzel, Jan Robert and Lammers, Twan and Kiessling,
                    Fabian},
  Title           = {Imalytics Preclinical: {Interactive} Analysis of
                    Biomedical Volume Data},
  JournalTitle    = {Theranostics},
  Date            = {2016},
  DOI             = {10.7150/thno.13624},
  Keywords        = {Gremse-Selection},
  Number          = {3},
  Pages           = {328--341},
  Volume          = {6}
}

@Article{Gremse:745400,
  Author          = {Gremse, Felix and Küpper, Kerstin and Naumann, Uwe},
  Title           = {Memory-Efficient Sparse Matrix-Matrix Multiplication by
                    Row Merging on Many-Core Architectures},
  JournalTitle    = {SIAM J. Sci. Comput.},
  Date            = {2018},
  DOI             = {10.1137/17m1121378},
  Keywords        = {Gremse-Selection},
  Number          = {4},
  Pages           = {C429--C449},
  Volume          = {40}
}

@Article{Gross2018,
  Author          = {Gross, Annika and Pack, Lotta A. P. and Schacht, Gabriel
                    M. and Kant, Sebastian and Ungewiss, Hanna and Meir,
                    Michael and Schlegel, Nicolas and Preisinger, Christian
                    and Boor, Peter and Guldiken, Nurdan and Krusche, Claudia
                    A. and Sellge, Gernot and Trautwein, Christian and
                    Waschke, Jens and Heuser, Arnd and Leube, Rudolf E. and
                    Strnad, Pavel},
  Title           = {Desmoglein 2, but not desmocollin 2, protects intestinal
                    epithelia from injury},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2018},
  DOI             = {10.1038/s41385-018-0062-z},
  Keywords        = {Guldiken-Selection},
  Number          = {6},
  Pages           = {1630--1639},
  Volume          = {11}
}

@Article{Grossi1985-nf,
  Author          = {Grossi, C E and Velardi, A and Cooper, M D},
  Title           = {Postnatal liver hemopoiesis in mice: {Generation} of
                    pre-B cells, granulocytes, and erythrocytes in discrete
                    colonies},
  JournalTitle    = {J. Immunol.},
  Date            = {1985},
  Number          = {4},
  Pages           = {2303--2311},
  Volume          = {135}
}

@Article{Gu2022-nf,
  Author          = {Gu, Wenyi and Hortlik, Hannah and Erasmus, Hans-Peter
                    and Schaaf, Louisa and Zeleke, Yasmin and Uschner, Frank
                    E and Ferstl, Philip and Schulz, Martin and Peiffer,
                    Kai-Henrik and Queck, Alexander and Sauerbruch, Tilman
                    and Brol, Maximilian Joseph and Rohde, Gernot and
                    Sanchez, Cristina and Moreau, Richard and Arroyo, Vicente
                    and Zeuzem, Stefan and Welsch, Christoph and Trebicka,
                    Jonel},
  Title           = {Trends and the course of liver cirrhosis and its
                    complications in Germany: Nationwide population-based
                    study (2005 to 2018)},
  JournalTitle    = {Lancet Reg Health Eur},
  Date            = {2022},
  DOI             = {10.1016/j.lanepe.2021.100240},
  Keywords        = {Trebicka-Selection},
  Number          = {100240},
  Pages           = {100240},
  Volume          = {12}
}

@Article{Guilliams2022-sq,
  Author          = {Guilliams, Martin and Bonnardel, Johnny and Haest,
                    Birthe and Vanderborght, Bart and Wagner, Camille and
                    Remmerie, Anneleen and Bujko, Anna and Martens, Liesbet
                    and Thoné, Tinne and Browaeys, Robin and De Ponti,
                    Federico F. and Vanneste, Bavo and Zwicker, Christian and
                    Svedberg, Freya R. and Vanhalewyn, Tineke and Gonçalves,
                    Amanda and Lippens, Saskia and Devriendt, Bert and Cox,
                    Eric and Ferrero, Giuliano and Wittamer, Valerie and
                    Willaert, Andy and Kaptein, Suzanne J.F. and Neyts, Johan
                    and Dallmeier, Kai and Geldhof, Peter and Casaert, Stijn
                    and Deplancke, Bart and ten Dijke, Peter and Hoorens,
                    Anne and Vanlander, Aude and Berrevoet, Frederik and Van
                    Nieuwenhove, Yves and Saeys, Yvan and Saelens, Wouter and
                    Van Vlierberghe, Hans and Devisscher, Lindsey and Scott,
                    Charlotte L.},
  Title           = {Spatial proteogenomics reveals distinct and
                    evolutionarily conserved hepatic macrophage niches},
  JournalTitle    = {Cell},
  Date            = {2022},
  DOI             = {10.1016/j.cell.2021.12.018},
  Number          = {2},
  Pages           = {379--396.e38},
  Volume          = {185}
}

@Article{Guillot2019-go,
  Author          = {Guillot, Adrien and Tacke, Frank},
  Title           = {Liver Macrophages: {Old} Dogmas and New Insights},
  JournalTitle    = {Hepatology Communications},
  Date            = {2019},
  DOI             = {10.1002/hep4.1356},
  Number          = {6},
  Pages           = {730--743},
  Volume          = {3}
}

@Article{Guillot2021-sz,
  Author          = {Guillot, Adrien and Guerri, Lucia and Feng, Dechun and
                    Kim, Seung-Jin and Ahmed, Yeni Ait and Paloczi, Janos and
                    He, Yong and Schuebel, Kornel and Dai, Shen and Liu,
                    Fengming and Pacher, Pal and Kisseleva, Tatiana and Qin,
                    Xuebin and Goldman, David and Tacke, Frank and Gao, Bin},
  Title           = {Bile acid-activated macrophages promote biliary
                    epithelial cell proliferation through integrin
                    $\alpha$v$\beta$6 upregulation following liver injury},
  JournalTitle    = {J. Clin. Invest.},
  Addendum        = preliminarywork,
  Date            = {2021},
  DOI             = {10.1172/jci132305},
  Number          = {9},
  Volume          = {131}
}

@Article{Guillot:791928,
  Author          = {Guillot, Adrien and Tacke, Frank},
  Title           = {The Unexpected Role of Neutrophils for Resolving Liver
                    Inflammation by Transmitting Micro{RNA}‐223 to
                    Macrophages},
  JournalTitle    = {Hepatology},
  Date            = {2020},
  DOI             = {10.1002/hep.30925},
  Keywords        = {,CRC1382-Project B05,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {749--751},
  Volume          = {71}
}

@Article{Guillot:808892,
  Author          = {Guillot, Adrien and Kohlhepp, Marlene S. and Bruneau,
                    Alix and Heymann, Felix and Tacke, Frank},
  Title           = {Deciphering the Immune Microenvironment on A Single
                    Archival Formalin-Fixed Paraffin-Embedded Tissue Section
                    by An Immediately Implementable Multiplex Fluorescence
                    Immunostaining Protocol},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2020},
  DOI             = {10.3390/cancers12092449},
  Keywords        = {,CRC1382-Project B05,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {9},
  Pages           = {2449},
  Volume          = {12}
}

@Article{Piano2019-ir,
  Author          = {Piano, Salvatore and Singh, Virendra and Caraceni, Paolo
                    and Maiwall, Rakhi and Alessandria, Carlo and Fernandez,
                    Javier and Soares, Elza Cotrim and Kim, Dong Joon and
                    Kim, Sung Eun and Marino, Monica and Vorobioff, Julio and
                    Barea, Rita de Cassia Ribeiro and Merli, Manuela and
                    Elkrief, Laure and Vargas, Victor and Krag, Aleksander
                    and Singh, Shivaram Prasad and Lesmana, Laurentius
                    Adrianto and Toledo, Claudio and Marciano, Sebastian and
                    Verhelst, Xavier and Wong, Florence and Intagliata,
                    Nicolas and Rabinowich, Liane and Colombato, Luis and
                    Kim, Sang Gyune and Gerbes, Alexander and Durand,
                    Francois and Roblero, Juan Pablo and Bhamidimarri, Kalyan
                    Ram and Boyer, Thomas D. and Maevskaya, Marina and
                    Fassio, Eduardo and Kim, Hyoung Su and Hwang, Jae Seok
                    and Gines, Pere and Gadano, Adrian and Sarin, Shiv Kumar
                    and Angeli, Paolo and Bartoletti, Michele and Brodersen,
                    Carlos and Bruns, Tony and de Man, Robert A. and Fialla,
                    Annette Dam and Gambino, Carmine and Gautam, Vikas and
                    Girala, Marcos and Juanola, Adria and Kim, Jeong Han and
                    Kim, Tae Hun and Kumar, Pramod and Lattanzi, Barbara and
                    Lee, Tae Hee and Rinaldi Lesmana, Cosmas A. and Moreau,
                    Richard and Nath, Preetam and Navarro, Gustavo and Park,
                    Ji-Won and Pinero, Gisela and Pyrsopoulos, Nikolaos T.
                    and Restellini, Sophie and Romero, Gustavo and Sacco,
                    Marco and Sevá-Pereira, Tiago and Simón-Talero,
                    Macarena and Song, Do Seon and Suk, Ki Tae and Van
                    Vlierberghe, Hans and Yim, Sun Young and Yoon, Eileen
                    Laurel and Zaccherini, Giacomo},
  Title           = {Epidemiology and Effects of Bacterial Infections in
                    Patients With Cirrhosis Worldwide},
  JournalTitle    = {Gastroenterology},
  Date            = {2019},
  DOI             = {10.1053/j.gastro.2018.12.005},
  Keywords        = {Global; Resistance; Sepsis; Stewardship},
  Number          = {5},
  Pages           = {1368--1380.e10},
  Volume          = {156}
}

@Article{Wong2021-tm,
  Author          = {Wong, Florence and Piano, Salvatore and Singh, Virendra
                    and Bartoletti, Michele and Maiwall, Rakhi and
                    Alessandria, Carlo and Fernandez, Javier and Soares, Elza
                    Cotrim and Kim, Dong Joon and Kim, Sung Eun and Marino,
                    Monica and Vorobioff, Julio and Barea, Rita de Cassia
                    Ribeiro and Merli, Manuela and Elkrief, Laure and Vargas,
                    Victor and Krag, Aleksander and Singh, Shivaram Prasad
                    and Lesmana, Laurentius Adrianto and Toledo, Claudio and
                    Marciano, Sebastian and Verhelst, Xavier and Intagliata,
                    Nicolas and Rabinowich, Liane and Colombato, Luis and
                    Kim, Sang Gyune and Gerbes, Alexander and Durand,
                    Francois and Roblero, Juan Pablo and Bruns, Tony and
                    Yoon, Eileen Laurel and Girala, Marcos and Pyrsopoulos,
                    Nikolaos T. and Kim, Tae Hun and Yim, Sun Young and
                    Juanola, Adria and Gadano, Adrian and Angeli, Paolo and
                    Bhamidimarri, Kalyan and Boyer, Thomas D. and Brodersen,
                    Carlos and Campion, Daniela and Caraceni, Paolo and de
                    Man, Robert A. and Fassio, Eduardo and Fialla, Annette
                    Dam and Gambino, Carmine and Gautam, Vikas and Gines,
                    Pere and Hwang, Jae Seok and Kim, Hyoung Su and Kim,
                    Jeong Han and Kumar, Pramod and Lattanz, Barbara and Lee,
                    Tae Hee and Rinaldi Lesmana, Cosmas A. and Maevskaya,
                    Marina and Nath, Preetam and Navarro, Gustavo and Park,
                    Ji-Won and Pinero, Gisela and Restellini, Sophie and
                    Romero, Gustavo and Sevá -Pereira, Tiago and
                    Simón-Talero, Macarena and Song, Do Seon and Suk, Ki Tae
                    and Van Vlierberghe, Hans and Zaccherini, Giacomo},
  Title           = {Clinical features and evolution of bacterial
                    infection-related acute-on-chronic liver failure},
  JournalTitle    = {J. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jhep.2020.07.046},
  Number          = {2},
  Pages           = {330--339},
  Volume          = {74}
}

@Article{Guldiken2019-uu,
  Author          = {Guldiken, Nurdan and Hamesch, Karim and Schuller, Shari
                    Malan and Aly, Mahmoud and Lindhauer, Cecilia and
                    Schneider, Carolin V and Fromme, Malin and Trautwein,
                    Christian and Strnad, Pavel},
  Title           = {Mild iron overload as seen in individuals homozygous for
                    the alpha-1 antitrypsin {Pi*Z} variant does not promote
                    liver fibrogenesis in {HFE} knockout mice},
  JournalTitle    = {Cells},
  Addendum        = equalpreliminarywork,
  Date            = {2019},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.3390/cells8111415},
  Keywords        = {Guldiken-Selection},
  Number          = {11},
  Pages           = {1415},
  Volume          = {8}
}

@Article{Guldiken2021-fr,
  Author          = {Guldiken, Nurdan and Argemi, Josepmaria and Gurbuz,
                    Berivan and Atkinson, Stephen R and Oliverius, Martin and
                    Fila, Petr and Hamesch, Karim and Bruns, Tony and
                    Cabezas, Joaquı́n and Lozano, Juan J and Mann, Jelena
                    and Cao, Sheng and Mathurin, Philippe and Shah, Vijay H
                    and Trautwein, Christian and Thursz, Mark R and Bataller,
                    Ramon and Strnad, Pavel},
  Title           = {Serum transferrin as a biomarker of hepatocyte nuclear
                    factor 4 alpha activity and hepatocyte function in liver
                    diseases},
  JournalTitle    = {BMC Med.},
  Date            = {2021},
  Addendum        = equal,
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1186/s12916-021-01917-6},
  Keywords        = {Guldiken-Selection},
  Number          = {1},
  Pages           = {39},
  Volume          = {19}
}

@Article{Guldiken:466361,
  Author          = {Guldiken, Nurdan and Usachov, Valentyn and Levada,
                    Kateryna and Trautwein, Christian and Ziol, Marianne and
                    Nahon, Pierre and Strnad, Pavel},
  Title           = {Keratins 8 and 18 are type {II} acute-phase responsive
                    genes overexpressed in human liver disease},
  JournalTitle    = {Liver Int.},
  Date            = {2014},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1111/liv.12608},
  Addendum        = equal,
  Keywords        = {Guldiken-Selection},
  Number          = {4},
  Pages           = {1203--1212},
  Volume          = {35}
}

@Article{Guo2016-yf,
  Author          = {Guo, Chuansheng and Xie, Shujun and Chi, Zhexu and
                    Zhang, Jinhua and Liu, Yangyang and Zhang, Li and Zheng,
                    Mingzhu and Zhang, Xue and Xia, Dajing and Ke, Yuehai and
                    Lu, Linrong and Wang, Di},
  Title           = {Bile acids control inflammation and metabolic disorder
                    through inhibition of {NLRP3} inflammasome},
  JournalTitle    = {Immunity},
  Date            = {2016},
  DOI             = {10.1016/j.immuni.2016.10.009},
  Number          = {4},
  Pages           = {802--816},
  Volume          = {45}
}

@Article{Guo2013-pg,
  Author          = {Guo, Shuhong and Al-Sadi, Rana and Said, Hamid M and Ma,
                    Thomas Y},
  Title           = {Lipopolysaccharide causes an increase in intestinal
                    tight junction permeability in vitro and in vivo by
                    inducing enterocyte membrane expression and localization
                    of {TLR-4} and {CD14}},
  JournalTitle    = {Am. J. Pathol.},
  Date            = {2013},
  DOI             = {10.1016/j.ajpath.2012.10.014},
  Number          = {2},
  Pages           = {375--387},
  Volume          = {182}
}

@Article{Guo2021,
  Author          = {Guo, Feifei and Estévez-Vázquez, Olga and
                    Benedé-Ubieto, Raquel and Maya-Miles, Douglas and Zheng,
                    Kang and Gallego-Durán, Rocío and Rojas, Ángela and
                    Ampuero, Javier and Romero-Gómez, Manuel and Philip,
                    Kaye and Egbuniwe, Isioma U. and Chen, Chaobo and Simon,
                    Jorge and Delgado, Teresa C. and Martínez-Chantar,
                    María Luz and Sun, Jie and Reissing, Johanna and Bruns,
                    Tony and Lamas-Paz, Arantza and Moral, Manuel Gómez del
                    and Woitok, Marius Maximilian and Vaquero, Javier and
                    Regueiro, José R. and Liedtke, Christian and Trautwein,
                    Christian and Bañares, Rafael and Cubero, Francisco
                    Javier and Nevzorova, Yulia A.},
  Title           = {A Shortcut from Metabolic-Associated Fatty Liver Disease
                    {(MAFLD)} to Hepatocellular Carcinoma {(HCC):} {C-myc} a
                    Promising Target for Preventative Strategies and
                    Individualized Therapy},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2021},
  DOI             = {10.3390/cancers14010192},
  Number          = {1},
  Pages           = {192},
  Volume          = {14}
}

@Article{Guo:753946,
  Author          = {Guo, Feifei and Zheng, Kang and Benedé-Ubieto, Raquel
                    and Cubero, Francisco Javier and Nevzorova, Yulia A.},
  Title           = {The Lieber-{DeCarli} Diet-A Flagship Model for
                    Experimental Alcoholic Liver Disease},
  JournalTitle    = {Alcohol.: Clin. Exp. Res.},
  Date            = {2018},
  DOI             = {10.1111/acer.13840},
  Keywords        = {Nevzorova-Selection},
  Number          = {10},
  Pages           = {1828--1840},
  Subtitle        = {A Flagship Model for Experimental Alcoholic Liver
                    Disease},
  Volume          = {42}
}

@Article{Tsiaoussis2018-md,
  Author          = {Tsiaoussis, Georgios I. and Papaioannou, Eleni C. and
                    Kourea, Eleni P. and Assimakopoulos, Stelios F. and
                    Theocharis, Georgios I. and Petropoulos, Michalis and
                    Theopistos, Vasileios I. and Diamantopoulou, Georgia G.
                    and Lygerou, Zoi and Spiliopoulou, Iris and Thomopoulos,
                    Konstantinos C.},
  Title           = {Expression of α-Defensins, {CD20+} B-lymphocytes, and
                    Intraepithelial {CD3+} T-lymphocytes in the Intestinal
                    Mucosa of Patients with Liver Cirrhosis: {Emerging}
                    Mediators of Intestinal Barrier Function},
  JournalTitle    = {Dig. Dis. Sci.},
  Date            = {2018},
  DOI             = {10.1007/s10620-018-5146-9},
  Number          = {10},
  Pages           = {2582--2592},
  Volume          = {63}
}

@Article{Gupta2022-yz,
  Author          = {Gupta, Biki and Rai, Ravi and Oertel, Michael and
                    Raeman, Reben},
  Title           = {Intestinal Barrier Dysfunction in Fatty Liver Disease:
                    {Roles} of Microbiota, Mucosal Immune System, and Bile
                    Acids},
  JournalTitle    = {Semin. Liver Dis.},
  Date            = {2022},
  DOI             = {10.1055/s-0042-1748037},
  Number          = {02},
  Pages           = {122--137},
  Volume          = {42}
}

@Article{Gupta1997Bile,
  Author          = {Gupta, S and Chowdhury, R},
  Title           = {Bile affects production of virulence factors and
                    motility of Vibrio cholerae},
  JournalTitle    = {Infect. Immun.},
  Date            = {1997-03},
  DOI             = {10.1128/iai.65.3.1131-1134.1997},
  Number          = {3},
  Pages           = {1131--1134},
  Volume          = {65}
}

@Article{Haange2012,
  Author          = {Haange, Sven-Bastiaan and Oberbach, Andreas and
                    Schlichting, Nadine and Hugenholtz, Floor and Smidt,
                    Hauke and von Bergen, Martin and Till, Holger and
                    Seifert, Jana},
  Title           = {Metaproteome Analysis and Molecular Genetics of Rat
                    Intestinal Microbiota Reveals Section and Localization
                    Resolved Species Distribution and Enzymatic
                    Functionalities},
  JournalTitle    = {J. Proteome Res.},
  Date            = {2012},
  DOI             = {10.1021/pr3006364},
  Number          = {11},
  Pages           = {5406--5417},
  Volume          = {11}
}

@Article{Haange2022-ui,
  Author          = {Haange, Sven-Bastiaan and Till, Andreas and Bergh,
                    Per-Olof and Fauler, Günter and Gigl, Michael and
                    Löfgren-Sandblom, Anita and Schaap, Frank G. and Clavel,
                    Thomas and Trautwein, Christian and Fenske, Wiebke and
                    Kleigrewe, Karin and Marschall, Hanns-Ulrich and Olde
                    Damink, Steven W. M. and Moustafa, Tarek and von Bergen,
                    Martin and Rolle-Kampczyk, Ulrike},
  Title           = {Ring Trial on Quantitative Assessment of Bile Acids
                    Reveals a Method- and Analyte-Specific Accuracy and
                    Reproducibility},
  JournalTitle    = {Metabolites},
  Date            = {2022},
  Keywords        = {von Bergen-Selection},
  DOI             = {10.3390/metabo12070583},
  ids             = {Haange:849341,Haange2022-en},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {7},
  Pages           = {583},
  Volume          = {12}
}

@Article{Habtezion2016-st,
  Author          = {Habtezion, Aida and Nguyen, Linh P and Hadeiba, Husein
                    and Butcher, Eugene C},
  Title           = {Leukocyte trafficking to the small intestine and colon},
  JournalTitle    = {Gastroenterology},
  Date            = {2016},
  DOI             = {10.1053/j.gastro.2015.10.046},
  Keywords        = {Adhesion Molecules; Chemokine Receptors; Intestine;
                    Leukocyte Trafficking},
  Number          = {2},
  Pages           = {340--354},
  Volume          = {150}
}

@Article{Hadis:176006,
  Author          = {Hadis, Usriansyah and Wahl, Benjamin and Schulz, Olga
                    and Hardtke-Wolenski, Matthias and Schippers, Angela and
                    Wagner, Norbert and Müller, Werner and Sparwasser, Tim
                    and Förster, Reinhold and Pabst, Oliver},
  Title           = {Intestinal Tolerance Requires Gut Homing and Expansion
                    of {FoxP3+} Regulatory T Cells in the Lamina Propria},
  JournalTitle    = {Immunity},
  Date            = {2011},
  DOI             = {10.1016/j.immuni.2011.01.016},
  ids             = {hadis2011a},
  Keywords        = {Pabst-Selection,Schippers-Selection,Wagner-Selection},
  Number          = {2},
  Pages           = {237--246},
  Volume          = {34}
}

@Article{Halmschlag2019-iz,
  Author          = {Halmschlag, Birthe and Hoffmann, Kyra and Hanke, René
                    and Putri, Sastia P and Fukusaki, Eiichiro and Büchs,
                    Jochen and Blank, Lars M.},
  Title           = {Comparison of isomerase and Weimberg pathway for
                    {$\gamma$-PGA} production from xylose by engineered
                    Bacillus subtilis},
  JournalTitle    = {Front. Bioeng. Biotechnol.},
  Date            = {2019},
  DOI             = {10.3389/fbioe.2019.00476},
  Keywords        = {Blank-Selection},
  Pages           = {476},
  Volume          = {7}
}

@Article{Fromme2022-ag,
  Author          = {Fromme, Malin and Schneider, Carolin V. and Trautwein,
                    Christian and Brunetti-Pierri, Nicola and Strnad, Pavel},
  Title           = {Alpha-1 antitrypsin deficiency: {A} re-surfacing adult
                    liver disorder},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2021.11.022},
  Number          = {4},
  Pages           = {946--958},
  Volume          = {76}
}

@Article{Halmschlag2019-yc,
  Author          = {Halmschlag, Birthe and Steurer, Xenia and Putri, Sastia
                    P and Fukusaki, Eiichiro and Blank, Lars M.},
  Title           = {Tailor-made poly-$\gamma$-glutamic acid production},
  JournalTitle    = {Metab. Eng.},
  Date            = {2019},
  DOI             = {10.1016/j.ymben.2019.07.009},
  Addendum        = preliminarywork,
  Keywords        = {Blank-Selection},
  Pages           = {239--248},
  Volume          = {55}
}

@Article{Hamesch2019-gx,
  Author          = {Hamesch, Karim and Mandorfer, Mattias and Pereira,
                    Vı́tor M and Moeller, Linda S and Pons, Monica and
                    Dolman, Grace E and Reichert, Matthias C and Schneider,
                    Carolin V. and Woditsch, Vivien and Voss, Jessica and
                    Lindhauer, Cecilia and Fromme, Malin and Spivak, Igor and
                    Guldiken, Nurdan and Zhou, Biaohuan and Arslanow, Anita
                    and Schaefer, Benedikt and Zoller, Heinz and Aigner,
                    Elmar and Reiberger, Thomas and Wetzel, Martin and
                    Siegmund, Britta and Simões, Carolina and Gaspar, Rui
                    and Maia, Luı́s and Costa, Dalila and Bento-Miranda,
                    Mário and van Helden, Josef and Yagmur, Eray and Bzdok,
                    Danilo and Stolk, Jan and Gleiber, Wolfgang and Knipel,
                    Verena and Windisch, Wolfram and Mahadeva, Ravi and Bals,
                    Robert and Koczulla, Rembert and Barrecheguren, Miriam
                    and Miravitlles, Marc and Janciauskiene, Sabina and
                    Stickel, Felix and Lammert, Frank and Liberal, Rodrigo
                    and Genesca, Joan and Griffiths, William J and Trauner,
                    Michael and Krag, Aleksander and Trautwein, Christian and
                    Strnad, Pavel and {European Alpha1-Liver Study Group}},
  Title           = {Liver fibrosis and metabolic alterations in adults with
                    alpha-1-antitrypsin deficiency caused by the {Pi*ZZ}
                    mutation},
  JournalTitle    = {Gastroenterology},
  Addendum        = preliminarywork,
  Date            = {2019},
  DOI             = {10.1053/j.gastro.2019.05.013},
  Keywords        = {Guldiken-Selection,Strnad-Selection},
  Number          = {3},
  Pages           = {705--719.e18},
  Volume          = {157}
}

@Article{Hamesch2020-pn,
  Author          = {Hamesch, Karim and Guldiken, Nurdan and Aly, Mahmoud and
                    Hüser, Norbert and Hartmann, Daniel and Rufat, Pierre
                    and Ziol, Marianne and Remih, Katharina and Lurje, Georg
                    and Scheiner, Bernhard and Trautwein, Christian and
                    Mandorfer, Mattias and Reiberger, Thomas and Mueller,
                    Sebastian and Bruns, Tony and Nahon, Pierre and Strnad,
                    Pavel},
  Title           = {Serum keratin 19 ({CYFRA21-1}) links ductular reaction
                    with portal hypertension and outcome of various advanced
                    liver diseases},
  JournalTitle    = {BMC Med.},
  Date            = {2020},
  Addendum        = equalpreliminarywork,
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1186/s12916-020-01784-7},
  Keywords        = {Guldiken-Selection},
  Number          = {1},
  Pages           = {336},
  Volume          = {18}
}

@Article{Hamzah:164430,
  Author          = {Hamzah, Juliana and Jugold, Manfred and Kiessling,
                    Fabian and Rigby, Paul and Manzur, Mitali and Marti, Hugo
                    H. and Rabie, Tamer and Kaden, Sylvia and Gröne,
                    Hermann-Josef and Hämmerling, Günter J. and Arnold,
                    Bernd and Ganss, Ruth},
  Title           = {Vascular normalization in Rgs5-deficient tumours
                    promotes immune destruction},
  JournalTitle    = {Nature},
  Date            = {2008},
  DOI             = {10.1038/nature06868},
  Number          = {7193},
  Pages           = {410--414},
  Volume          = {453}
}

@Article{Han2021-op,
  Author          = {Han, Tianyu and Nebelung, Sven and Pedersoli, Federico
                    and Zimmermann, Markus and Schulze-Hagen, Maximilian and
                    Ho, Michael and Haarburger, Christoph and Kiessling,
                    Fabian and Kuhl, Christiane and Schulz, Volkmar and
                    Truhn, Daniel},
  Title           = {Advancing diagnostic performance and clinical usability
                    of neural networks via adversarial training and dual
                    batch normalization},
  JournalTitle    = {Nat. Commun.},
  Date            = {2021},
  DOI             = {10.1038/s41467-021-24464-3},
  Keywords        = {Kießling-Selection},
  Number          = {1},
  Pages           = {4315},
  Volume          = {12}
}

@Article{Han2021-wp,
  Author          = {Han, Yong-Hyun and Onufer, Emily J. and Huang, Li-Hao
                    and Sprung, Robert W. and Davidson, W. Sean and
                    Czepielewski, Rafael S. and Wohltmann, Mary and
                    Sorci-Thomas, Mary G. and Warner, Brad W. and Randolph,
                    Gwendalyn J.},
  Title           = {Enterically derived high-density lipoprotein restrains
                    liver injury through the portal vein},
  JournalTitle    = {Science},
  Date            = {2021},
  DOI             = {10.1126/science.abe6729},
  Number          = {6553},
  Pages           = {eabe6729},
  Volume          = {373}
}

@Article{Hang2019-cn,
  Author          = {Hang, Saiyu and Paik, Donggi and Yao, Lina and Kim,
                    Eunha and Trinath, Jamma and Lu, Jingping and Ha, Soyoung
                    and Nelson, Brandon N and Kelly, Samantha P and Wu, Lin
                    and Zheng, Ye and Longman, Randy S and Rastinejad,
                    Fraydoon and Devlin, A Sloan and Krout, Michael R and
                    Fischbach, Michael A and Littman, Dan R and Huh, Jun R},
  Title           = {Bile acid metabolites control {TH17} and Treg cell
                    differentiation},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-019-1785-z},
  Number          = {7785},
  Pages           = {143--148},
  Volume          = {576}
}

@Article{Hanna2016,
  Author          = {Hanna, Daniel and Riedmaier, Ariane Emami and Sugamori,
                    Kim S. and Grant, Denis M.},
  Title           = {Influence of sex and developmental stage on acute
                    hepatotoxic and inflammatory responses to liver
                    procarcinogens in the mouse},
  JournalTitle    = {Toxicology},
  Date            = {2016},
  DOI             = {10.1016/j.tox.2016.10.006},
  Keywords        = {4-Aminobiphenyl; Diethylnitrosamine; Liver;
                    Hepatotoxicity; Inflammation; Nuclear factor erythroid
                    2-related factor 2; Sex differences},
  Pages           = {30--40},
  Volume          = {373}
}

@Article{Hao:716345,
  Author          = {Hao, Fengjie and Cubero, Francisco Javier and Ramadori,
                    Pierluigi and Liao, Lijun and Haas, Ute and Lambertz,
                    Daniela and Sonntag, Roland and Bangen, Jörg- Martin and
                    Gassler, Nikolaus and Hoss, Mareike and Streetz, Konrad L
                    and Reissing, Johanna and Zimmermann, Henning W and
                    Trautwein, Christian and Liedtke, Christian and
                    Nevzorova, Yulia A.},
  Title           = {Inhibition of Caspase-8 does not protect from
                    alcohol-induced liver apoptosis but alleviates alcoholic
                    hepatic steatosis in mice},
  JournalTitle    = {Cell Death Dis.},
  Date            = {2017},
  DOI             = {10.1038/cddis.2017.532},
  Keywords        = {Nevzorova-Selection},
  Number          = {10},
  Pages           = {e3152--e3152},
  Volume          = {8}
}

@Article{Hatting2015,
  Author          = {Hatting, M. and Spannbauer, M and Peng, J and Al
                    Masaoudi, M and Sellge, G and Nevzorova, Y. A. and
                    Gassler, N and Liedtke, C. and Cubero, F J and Trautwein,
                    C.},
  Title           = {Lack of gp130 expression in hepatocytes attenuates tumor
                    progression in the {DEN} model},
  JournalTitle    = {Cell Death Dis.},
  Date            = {2015},
  DOI             = {10.1038/cddis.2014.590},
  ids             = {Hatting:540880},
  Keywords        = {Hatting-Selection},
  Number          = {3},
  Pages           = {e1667--e1667},
  Volume          = {6}
}

@Article{Hatting:231729,
  Author          = {Hatting, Maximilian and Zhao, Gang and Schumacher,
                    Fabienne and Sellge, Gernot and Al Masaoudi, Malika and
                    Gaβler, Nikolaus and Boekschoten, Mark and Müller,
                    Michael and Liedtke, Christian and Cubero, Francisco
                    Javier and Trautwein, Christian},
  Title           = {Hepatocyte caspase-8 is an essential modulator of
                    steatohepatitis in rodents},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26271},
  Keywords        = {Hatting-Selection},
  Number          = {6},
  Pages           = {2189--2201},
  Volume          = {57}
}

@Article{Hatting:716366,
  Author          = {Hatting, Maximilian and Rines, Amy K. and Luo, Chi and
                    Tabata, Mitsuhisa and Sharabi, Kfir and Hall, Jessica A.
                    and Verdeguer, Francisco and Trautwein, Christian and
                    Puigserver, Pere},
  Title           = {Adipose Tissue {CLK2} Promotes Energy Expenditure during
                    High-Fat Diet Intermittent Fasting},
  JournalTitle    = {Cell Metab.},
  Date            = {2017},
  DOI             = {10.1016/j.cmet.2016.12.007},
  Keywords        = {Hatting-Selection},
  Number          = {2},
  Pages           = {428--437},
  Volume          = {25}
}

@Article{Hausen:834321,
  Author          = {Hausen, Daniela Adele and Bossert, Lukas C. and
                    Trautwein-Bruns, Ute},
  Title           = {Aufgaben- und Kompetenzspektrum der Data Stewards an der
                    {RWTH} Aachen University},
  JournalTitle    = {Bausteine Forschungsdatenmanagement},
  Date            = {2021},
  DOI             = {10.17192/bfdm.2021.3.8352},
  Options         = {openaccess=auto},
  doi+an:default  = {=openaccess},
  Keywords        = {,CRC1382-Project Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {92--105},
  Subtitle        = {Generell und explizit am Beispiel des
                    Sonderforschungsbereichs 1382},
  Volume          = {3}
}

@Article{Jin2013-jl,
  Author          = {Jin, Chengcheng and Henao-Mejia, Jorge and Flavell,
                    Richard A.},
  Title           = {Innate Immune Receptors: {Key} Regulators of Metabolic
                    Disease Progression},
  JournalTitle    = {Cell Metab.},
  Date            = {2013},
  DOI             = {10.1016/j.cmet.2013.05.011},
  Number          = {6},
  Pages           = {873--882},
  Volume          = {17}
}

@Article{Hayashi2001innate,
  Author          = {Hayashi, Fumitaka and Smith, Kelly D. and Ozinsky,
                    Adrian and Hawn, Thomas R. and Yi, Eugene C. and
                    Goodlett, David R. and Eng, Jimmy K. and Akira, Shizuo
                    and Underhill, David M. and Aderem, Alan},
  Title           = {The innate immune response to bacterial flagellin is
                    mediated by Toll-like receptor 5},
  JournalTitle    = {Nature},
  Date            = {2001},
  DOI             = {10.1038/35074106},
  Number          = {6832},
  Pages           = {1099--1103},
  Volume          = {410}
}

@Article{He2022-mp,
  Author          = {He, Shuying and Cui, Shudan and Song, Wen and Jiang,
                    Yonghong and Chen, Hongsheng and Liao, Dongjiang and Lu,
                    Xinpeng and Li, Jun and Chen, Xueqing and Peng, Liang},
  Title           = {Interleukin-17 Weakens the {NAFLD/NASH} Process by
                    Facilitating Intestinal Barrier Restoration Depending on
                    the Gut Microbiota},
  JournalTitle    = {mBio},
  Date            = {2022},
  DOI             = {10.1128/mbio.03688-21},
  Number          = {2},
  Pages           = {e0368821},
  Volume          = {13}
}

@Article{He2019-fl,
  Author          = {He, Shun and Kahles, Florian and Rattik, Sara and Nairz,
                    Manfred and McAlpine, Cameron S and Anzai, Atsushi and
                    Selgrade, Daniel and Fenn, Ashley M and Chan, Christopher
                    T and Mindur, John E and Valet, Colin and Poller, Wolfram
                    C and Halle, Lennard and Rotllan, Noemi and Iwamoto,
                    Yoshiko and Wojtkiewicz, Gregory R and Weissleder, Ralph
                    and Libby, Peter and Fernández-Hernando, Carlos and
                    Drucker, Daniel J and Nahrendorf, Matthias and Swirski,
                    Filip K},
  Title           = {Gut intraepithelial {T} cells calibrate metabolism and
                    accelerate cardiovascular disease},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-018-0849-9},
  Number          = {7742},
  Pages           = {115--119},
  Volume          = {566}
}

@Article{Heinrichs:462073,
  Author          = {Heinrichs, Daniel and Berres, Marie‐Luise and Coeuru,
                    Melanie and Knauel, Meike and Nellen, Andreas and
                    Fischer, Petra and Philippeit, Claudia and Bucala,
                    Richard and Trautwein, Christian and Wasmuth, Hermann E.
                    and Bernhagen, Jürgen},
  Title           = {Protective role of macrophage migration inhibitory
                    factor in nonalcoholic steatohepatitis},
  JournalTitle    = {The FASEB Journal},
  Date            = {2014},
  DOI             = {10.1096/fj.14-256776},
  Number          = {12},
  Pages           = {5136--5147},
  Volume          = {28}
}

@Article{Heinrichs:811474,
  Author          = {Heinrichs, Daniel and Brandt, Elisa Fabiana and Fischer,
                    Petra and Köhncke, Janine and Wirtz, Theresa H. and
                    Guldiken, Nurdan and Djudjaj, Sonja and Boor, Peter and
                    Kroy, Daniela C. and Weiskirchen, Ralf and Bucala,
                    Richard and Wasmuth, Hermann E. and Strnad, Pavel and
                    Trautwein, Christian and Bernhagen, Jürgen and Berres,
                    Marie-Luise},
  Title           = {Unexpected Pro-Fibrotic Effect of {MIF} in Non-Alcoholic
                    Steatohepatitis Is Linked to a Shift in {NKT} Cell
                    Populations},
  JournalTitle    = {Cells},
  Date            = {2021},
  DOI             = {10.3390/cells10020252},
  ids             = {Heinrichs2021-dp},
  Keywords        = {Berres-Selection,CRC1382-Project B04,CRC1382-Project
                    B04,CRC1382-Project A03,CRC1382-Project
                    A03,CRC1382-Project A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {252},
  Volume          = {10}
}

@Article{Hemmers2022-zd,
  Author          = {Hemmers, Christian and Schulte, Corinna and Wollenhaupt,
                    Julia and Wong, Dickson W L and Harlacher, Eva and
                    Orth-Alampour, Setareh and Klinkhammer, Barbara Mara and
                    Schirmer, Stephan H and Böhm, Michael and Marx, Nikolaus
                    and Speer, Thimoteus and Boor, Peter and Jankowski,
                    Joachim and Noels, Heidi},
  Title           = {Chemokine {CCL9} is upregulated early in chronic kidney
                    disease and counteracts kidney inflammation and
                    fibrosis},
  JournalTitle    = {Biomedicines},
  Date            = {2022},
  DOI             = {10.3390/biomedicines10020420},
  Keywords        = {Noels-Selection},
  Number          = {2},
  Pages           = {420},
  Volume          = {10}
}

@Article{Henneke:828379,
  Author          = {Henneke, Philipp and Kierdorf, Katrin and Hall, Lindsay
                    J. and Sperandio, Markus and Hornef, Mathias W.},
  Title           = {Perinatal development of innate immune topology},
  JournalTitle    = {eLife},
  Date            = {2021},
  DOI             = {10.7554/eLife.67793},
  ids             = {Henneke2021-mo},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {e67793},
  Volume          = {10}
}

@Article{Herberth2015,
  Author          = {Herberth, Gunda and Offenberg, Kirsten and
                    Rolle-Kampczyk, Ulrike and Bauer, Mario and Otto,
                    Wolfgang and Röder, Stefan and Grützmann, Konrad and
                    Sack, Ulrich and Simon, Jan-Christoph and Borte, Michael
                    and von Bergen, Martin and Lehmann, Irina},
  Title           = {Endogenous metabolites and inflammasome activity in
                    early childhood and links to respiratory diseases},
  JournalTitle    = {J. Allergy Clin. Immun.},
  Date            = {2015},
  DOI             = {10.1016/j.jaci.2015.01.022},
  Number          = {2},
  Pages           = {495--497},
  Volume          = {136}
}

@Article{Hermann2020-oq,
  Author          = {Hermann, Juliane and Noels, Heidi and Theelen, Wendy and
                    Lellig, Michaela and Orth-Alampour, Setareh and Boor,
                    Peter and Jankowski, Vera and Jankowski, Joachim},
  Title           = {Sample preparation of formalin-fixed paraffin-embedded
                    tissue sections for {MALDI-mass} spectrometry imaging},
  JournalTitle    = {Anal. Bioanal. Chem.},
  Date            = {2020},
  DOI             = {10.1007/s00216-019-02296-x},
  Keywords        = {Formalin-fixed paraffin-embedded tissue sections; MALDI
                    imaging; Optimized sample standard operating protocols
                    (SOP); Tissue preparation},
  Number          = {6},
  Addendum        = preliminarywork,
  Pages           = {1263--1275},
  Volume          = {412}
}

@Article{Hermann2021-mo,
  Author          = {Hermann, Juliane and Brehmer, Kai and Jankowski, Vera
                    and Lellig, Michaela and Hohl, Mathias and Mahfoud, Felix
                    and Speer, Timotheus and Schunk, Stefan J and Tschernig,
                    Thomas and Thiele, Herbert and Jankowski, Joachim},
  Title           = {Registration of image modalities for analyses of tissue
                    samples using {3D} image modelling},
  JournalTitle    = {Proteomics Clin. Appl.},
  Date            = {2021},
  DOI             = {10.1002/prca.201900143},
  Keywords        = {3D model; matrix-assisted laser desorption/ionization
                    mass spectrometry imaging (MALDI MSI); multimodal
                    imaging; registration},
  Number          = {1},
  Pages           = {e1900143},
  Addendum        = preliminarywork,
  Volume          = {15}
}

@Article{Hernandez-Chirlaque2016-iy,
  Author          = {Hernández-Chirlaque, Cristina and Aranda, Carlos J. and
                    Ocón, Borja and Capitán-Cañadas, Fermín and
                    Ortega-González, Mercedes and Carrero, Juan Jesús and
                    Suárez, María Dolores and Zarzuelo, Antonio and
                    Sánchez de Medina, Fermín and Martínez-Augustin,
                    Olga},
  Title           = {Germ-free and Antibiotic-treated Mice are Highly
                    Susceptible to Epithelial Injury in {DSS} Colitis},
  JournalTitle    = {J. Crohns. Colitis},
  Date            = {2016},
  DOI             = {10.1093/ecco-jcc/jjw096},
  Number          = {11},
  Pages           = {1324--1335},
  Volume          = {10}
}

@Article{Heymann:572509,
  Author          = {Heymann, Felix and Peusquens, Julia and
                    Ludwig‐Portugall, Isis and Kohlhepp, Marlene and Ergen,
                    Can and Niemietz, Patricia and Martin, Christian and van
                    Rooijen, Nico and Ochando, Jordi C. and Randolph,
                    Gwendalyn J. and Luedde, Tom and Ginhoux, Florent and
                    Kurts, Christian and Trautwein, Christian and Tacke,
                    Frank},
  Title           = {Liver inflammation abrogates immunological tolerance
                    induced by Kupffer cells},
  JournalTitle    = {Hepatology},
  Date            = {2015},
  DOI             = {10.1002/hep.27793},
  ids             = {heymann2015a},
  Keywords        = {Tacke-Selection},
  Number          = {1},
  Pages           = {279--291},
  Volume          = {62}
}

@Article{Heymann:685011,
  Author          = {Heymann, Felix and Tacke, Frank},
  Title           = {Immunology in the liver — from homeostasis to
                    disease},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2016},
  DOI             = {10.1038/nrgastro.2015.200},
  Keywords        = {Tacke-Selection},
  Number          = {2},
  Pages           = {88--110},
  Subtitle        = {From homeostasis to disease},
  Volume          = {13}
}

@Article{Hintsche2017polar,
  Author          = {Hintsche, Marius and Waljor, Veronika and Großmann,
                    Robert and Kühn, Marco J. and Thormann, Kai M. and
                    Peruani, Fernando and Beta, Carsten},
  Title           = {A polar bundle of flagella can drive bacterial swimming
                    by pushing, pulling, or coiling around the cell body},
  JournalTitle    = {Sci. Rep.},
  Date            = {2017-12},
  DOI             = {10.1038/s41598-017-16428-9},
  Note            = {[Online; accessed 2018-03-06]},
  Number          = {1},
  Volume          = {7}
}

@Article{Hitch:819354,
  Author          = {Hitch, Thomas C. A. and Riedel, Thomas and Oren, Aharon
                    and Overmann, Jörg and Lawley, Trevor D. and Clavel,
                    Thomas},
  Title           = {Automated analysis of genomic sequences facilitates
                    high-throughput and comprehensive description of
                    bacteria},
  JournalTitle    = {ISME communications},
  Date            = {2021},
  DOI             = {10.1038/s43705-021-00017-z},
  Keywords        = {Clavel-Selection,CRC1382-Project A05,CRC1382-Project
                    Q02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {16},
  Volume          = {1}
}

@Article{Isensee2021-ax,
  Author          = {Isensee, Fabian and Jaeger, Paul F. and Kohl, Simon A.
                    A. and Petersen, Jens and Maier-Hein, Klaus H.},
  Title           = {{nnU}-Net: {A} self-configuring method for deep
                    learning-based biomedical image segmentation},
  JournalTitle    = {Nat. Methods},
  Date            = {2020},
  DOI             = {10.1038/s41592-020-01008-z},
  Number          = {2},
  Pages           = {203--211},
  Volume          = {18}
}

@Article{Hogstad:753945,
  Author          = {Hogstad, Brandon and Berres, Marie-Luise and
                    Chakraborty, Rikhia and Tang, Jun and Bigenwald, Camille
                    and Serasinghe, Madhavika and Lim, Karen Phaik Har and
                    Lin, Howard and Man, Tsz-Kwong and Remark, Romain and
                    Baxter, Samantha and Kana, Veronika and Jordan, Stefan
                    and Karoulia, Zoi and Kwan, Wing-hong and Leboeuf,
                    Marylene and Brandt, Elisa and Salmon, Helene and
                    McClain, Kenneth and Poulikakos, Poulikos and Chipuk,
                    Jerry and Mulder, Willem J.M. and Allen, Carl E. and
                    Merad, Miriam},
  Title           = {{RAF/MEK/extracellular} signal-related kinase pathway
                    suppresses dendritic cell migration and traps dendritic
                    cells in {Langerhans} cell histiocytosis lesions},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2017},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1084/jem.20161881},
  Addendum        = equalpreliminarywork,
  ids             = {Hogstad2018-na},
  Keywords        = {Berres-Selection},
  Number          = {1},
  Pages           = {319--336},
  ShortJournal    = {JEM},
  Volume          = {215}
}

@Article{Holmar:807156,
  Author          = {Holmar, Jana and de la Puente-Secades, Sofia and Floege,
                    Jürgen and Noels, Heidi and Jankowski, Joachim and
                    Orth-Alampour, Setareh},
  Title           = {Uremic Toxins Affecting Cardiovascular Calcification: A
                    Systematic Review},
  JournalTitle    = {Cells},
  Date            = {2020},
  DOI             = {10.3390/cells9112428},
  Keywords        = {,CRC1382-Project A04,CRC1382-Project A04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {11},
  Pages           = {2428},
  Volume          = {9}
}

@TechReport{Clasen2022Silent,
  Author          = {Clasen, Sara J. and Bell, Michael E. W. and Lee, Du-Hwa
                    and Henseler, Zachariah M. and Borbón, Andrea and de la
                    Cuesta-Zuluaga, Jacobo and Parys, Katarzyna and Zou, Jun
                    and Youngblut, Nicholas D. and Gewirtz, Andrew T. and
                    Belkhadir, Youssef and Ley, Ruth E.},
  Title           = {Silent recognition of flagellins from human gut
                    commensal bacteria by Toll-like receptor 5},
  Date            = {2022-04-12},
  DOI             = {10.1101/2022.04.12.488020}
}

@Article{Hong2017-nu,
  Author          = {Hong, Chun-Pyo and Park, Areum and Yang, Bo-Gie and Yun,
                    Chang Ho and Kwak, Min-Jung and Lee, Gil-Woo and Kim,
                    Jung-Hwan and Jang, Min Seong and Lee, Eun-Jung and Jeun,
                    Eun-Ji and You, Gihoon and Kim, Kwang Soon and Choi,
                    Youngwoo and Park, Ji-Hwan and Hwang, Daehee and Im,
                    Sin-Hyeog and Kim, Jihyun F and Kim, Yoon-Keun and Seoh,
                    Ju-Young and Surh, Charles D and Kim, You-Me and Jang,
                    Myoung Ho},
  Title           = {Gut-specific delivery of T-helper 17 cells reduces
                    obesity and insulin resistance in mice},
  JournalTitle    = {Gastroenterology},
  Date            = {2017},
  DOI             = {10.1053/j.gastro.2017.02.016},
  Keywords        = {Glucose Tolerance; Intestinal Microbiota; Mucosal
                    Immunity},
  Number          = {8},
  Pages           = {1998--2010},
  Volume          = {152}
}

@Article{Hornef:781397,
  Author          = {Hornef, Mathias W. and Torow, Natalia},
  Title           = {‘Layered immunity’ and the ‘neonatal window of
                    opportunity’ - timed succession of non-redundant phases
                    to establish mucosal host-microbial homeostasis after
                    birth},
  JournalTitle    = {Immunology},
  Date            = {2020},
  DOI             = {10.1111/imm.13149},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {15--25},
  Volume          = {159}
}

@Article{Hou2020-gy,
  Author          = {Hou, Lei and Yang, Le and Chang, Na and Zhao, Xinhao and
                    Zhou, Xuan and Dong, Chengbin and Liu, Fuquan and Yang,
                    Lin and Li, Liying},
  Title           = {Macrophage Sphingosine 1-Phosphate Receptor 2 Blockade
                    Attenuates Liver Inflammation and Fibrogenesis Triggered
                    by {NLRP3} Inflammasome},
  JournalTitle    = {Front. Immunol.},
  Date            = {2020},
  DOI             = {10.3389/fimmu.2020.01149},
  Pages           = {1149},
  Volume          = {11}
}

@Article{Houston2015,
  Author          = {Houston, S A and Cerovic, V and Thomson, C and Brewer, J
                    and Mowat, A M and Milling, S},
  Title           = {The lymph nodes draining the small intestine and colon
                    are anatomically separate and immunologically distinct},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2015},
  DOI             = {10.1038/mi.2015.77},
  Keywords        = {Cerovic-Selection},
  Number          = {2},
  Pages           = {468--478},
  Volume          = {9}
}

@Article{Hu2020Remarkable,
  Author          = {Hu, Dalong and Reeves, Peter R.},
  Title           = {The Remarkable Dual-Level Diversity of Prokaryotic
                    Flagellins},
  JournalTitle    = {mSystems},
  Date            = {2020-02-11},
  DOI             = {10.1128/msystems.00705-19},
  Editor          = {Zhaxybayeva, Olga},
  Number          = {1},
  Pages           = {e00705--19},
  Volume          = {5}
}

@Article{Hu:230343,
  Author          = {Hu, Wei and Nevzorova, Yulia A. and Haas, Ute and Moro,
                    Nives and Sicinski, Piotr and Geng, Yan and Barbacid,
                    Mariano and Trautwein, Christian and Liedtke, Christian},
  Title           = {Concurrent deletion of cyclin E1 and cyclin-dependent
                    kinase 2 in hepatocytes inhibits {DNA} replication and
                    liver regeneration in mice},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26584},
  Keywords        = {Liedtke-Selection,Nevzorova-Selection},
  Number          = {2},
  Pages           = {651--660},
  Subtitle        = {Hu et al.},
  Volume          = {59}
}

@Article{Huang2006-nw,
  Author          = {Huang, Wendong and Ma, Ke and Zhang, Jun and Qatanani,
                    Mohammed and Cuvillier, James and Liu, Jun and Dong,
                    Bingning and Huang, Xiongfei and Moore, David D.},
  Title           = {Nuclear Receptor-Dependent Bile Acid Signaling Is
                    Required for Normal Liver Regeneration},
  JournalTitle    = {Science},
  Date            = {2006},
  DOI             = {10.1126/science.1121435},
  Number          = {5771},
  Pages           = {233--236},
  Volume          = {312}
}

@Article{Huang2009Use,
  Author          = {Huang, Li-Yun and DuMontelle, James L. and Zolodz,
                    Melissa and Deora, Aparna and Mozier, Ned M. and Golding,
                    Basil},
  Title           = {Use of Toll-Like Receptor Assays To Detect and Identify
                    Microbial Contaminants in Biological Products},
  JournalTitle    = {J. Clin. Microbiol.},
  Date            = {2009-11},
  DOI             = {10.1128/jcm.00373-09},
  Number          = {11},
  Pages           = {3427--3434},
  Volume          = {47}
}

@Article{Huang2018-lf,
  Author          = {Huang, Xuan and Li, Yong and Fu, Mingui and Xin,
                    Hong-Bo},
  Title           = {Polarizing macrophages in vitro},
  JournalTitle    = {Methods Mol. Biol.},
  Date            = {2018},
  DOI             = {10.1007/978-1-4939-7837-3_12},
  Keywords        = {Adenosines; Glucocorticoids; IFN$\gamma$; IL-4; Immune
                    complexes; LPS; Macrophages; THP-1},
  Pages           = {119--126},
  Volume          = {1784}
}

@Article{Sonntag:846313,
  Author          = {Sonntag, Roland and Penners, Christian and Kohlhepp,
                    Marlene and Haas, Ute and Lambertz, Daniela and Kroh,
                    Andreas and Cramer, Thorsten and Ticconi, Fabio and
                    Costa, Ivan G. and Tacke, Frank and Gassler, Nikolaus and
                    Trautwein, Christian and Liedtke, Christian},
  Title           = {Cyclin E1 in Murine and Human Liver Cancer: A Promising
                    Target for Therapeutic Intervention during Tumour
                    Progression},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2021},
  Addendum        = preliminarywork,
  DOI             = {10.3390/cancers13225680},
  Keywords        = {,CRC1382-Project A02,CRC1382-Project Q03,CRC1382-Project
                    B05,CRC1382-Project A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {22},
  Pages           = {5680},
  Volume          = {13}
}

@Article{Hubbers2020-pc,
  Author          = {Hübbers, Anna and Hennings, Julia and Lambertz, Daniela
                    and Haas, Ute and Trautwein, Christian and Nevzorova,
                    Yulia A. and Sonntag, Roland and Liedtke, Christian},
  Title           = {Pharmacological Inhibition of Cyclin-Dependent Kinases
                    Triggers Anti-Fibrotic Effects in Hepatic Stellate Cells
                    In Vitro},
  JournalTitle    = {Int. J. Mol. Sci.},
  Addendum        = preliminarywork,
  Date            = {2020},
  DOI             = {10.3390/ijms21093267},
  Keywords        = {,CRC1382-Project A02,CRC1382-Project A02,CRC1382-Project
                    Q03,CRC1382-Project A02,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {9},
  Pages           = {3267},
  Volume          = {21}
}

@Article{Hundertmark2022-zf,
  Author          = {Hundertmark, Jana and Berger, Hilmar and Tacke, Frank},
  Title           = {Single cell {RNA} sequencing in {NASH}},
  JournalTitle    = {Methods Mol. Biol.},
  Date            = {2022},
  DOI             = {10.1007/978-1-0716-2128-8_15},
  Pages           = {181--202},
  Volume          = {2455}
}

@Article{Hundertmark:815766,
  Author          = {Hundertmark, Jana and Tacke, Frank},
  Title           = {How effective are nonalcoholic fatty liver disease
                    models for drug discovery?},
  JournalTitle    = {Expert Opin. Drug Discov.},
  Date            = {2020},
  DOI             = {10.1080/17460441.2020.1776258},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {11},
  Pages           = {1237--1240},
  Volume          = {15}
}

@Article{IbidapoObe:787168,
  Author          = {Ibidapo-obe, Oluwatomi and Stengel, Sven and
                    Köse-Vogel, Nilay and Quickert, Stefanie and Reuken,
                    Philipp A. and Busch, Martin and Bauer, Michael and
                    Stallmach, Andreas and Bruns, Tony},
  Title           = {Mucosal-Associated Invariant T Cells Redistribute to the
                    Peritoneal Cavity During Spontaneous Bacterial
                    Peritonitis and Contribute to Peritoneal Inflammation},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jcmgh.2020.01.003},
  Keywords        = {Bruns-Selection},
  Number          = {4},
  Pages           = {661--677},
  ShortJournal    = {CMGH},
  Volume          = {9}
}

@Article{Yarbakht2019-mq,
  Author          = {Yarbakht, Melina and Pradhan, Pranita and Köse-Vogel,
                    Nilay and Bae, Hyeonsoo and Stengel, Sven and Meyer,
                    Tobias and Schmitt, Michael and Stallmach, Andreas and
                    Popp, Jürgen and Bocklitz, Thomas Wilhelm and Bruns,
                    Tony},
  Title           = {Nonlinear Multimodal Imaging Characteristics of Early
                    Septic Liver Injury in a Mouse Model of Peritonitis},
  JournalTitle    = {Anal. Chem.},
  Date            = {2019},
  DOI             = {10.1021/acs.analchem.9b01746},
  Number          = {17},
  Pages           = {11116--11121},
  Volume          = {91}
}

@Article{Ikenaga2015-if,
  Author          = {Ikenaga, Naoki and Liu, Susan B. and Sverdlov, Deanna Y.
                    and Yoshida, Shuhei and Nasser, Imad and Ke, Qingen and
                    Kang, Peter M. and Popov, Yury},
  Title           = {A New Mdr2\textsuperscript{-/-} Mouse Model of
                    Sclerosing Cholangitis with Rapid Fibrosis Progression,
                    Early-Onset Portal Hypertension, and Liver Cancer},
  JournalTitle    = {Am. J. Pathol.},
  Date            = {2015},
  DOI             = {10.1016/j.ajpath.2014.10.013},
  Number          = {2},
  Pages           = {325--334},
  Volume          = {185}
}

@Article{Innes:837765,
  Author          = {Innes, Hamish and Nischalke, Hans Dieter and Guha, Indra
                    Neil and Weiss, Karl Heinz and Irving, Will and
                    Gotthardt, Daniel and Barnes, Eleanor and Fischer, Janett
                    and Ansari, M. Azim and Rosendahl, Jonas and Lin,
                    Shang-Kuan and Marot, Astrid and Pedergnana, Vincent and
                    Casper, Markus and Benselin, Jennifer and Lammert, Frank
                    and McLauchlan, John and Lutz, Philip L. and Hamill,
                    Victoria and Mueller, Sebastian and Morling, Joanne R.
                    and Semmler, Georg and Eyer, Florian and von Felden,
                    Johann and Link, Alexander and Vogel, Arndt and
                    Marquardt, Jens U. and Sulk, Stefan and Trebicka, Jonel
                    and Valenti, Luca and Datz, Christian and Reiberger,
                    Thomas and Schafmayer, Clemens and Berg, Thomas and
                    Deltenre, Pierre and Hampe, Jochen and Stickel, Felix and
                    Buch, Stephan},
  Title           = {The rs429358 Locus in Apolipoprotein E Is Associated
                    With Hepatocellular Carcinoma in Patients With
                    Cirrhosis},
  JournalTitle    = {Hepatology Communications},
  Date            = {2021},
  DOI             = {10.1002/hep4.1886},
  Keywords        = {,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)}
}

@Article{Iwakiri:834276,
  Author          = {Iwakiri, Yasuko and Trebicka, Jonel},
  Title           = {Portal hypertension in cirrhosis},
  JournalTitle    = {JHEP Reports},
  Date            = {2021},
  DOI             = {10.1016/j.jhepr.2021.100316},
  Keywords        = {,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {100316},
  Subtitle        = {Pathophysiological mechanisms and therapy},
  Volume          = {3}
}

@Article{Jankowski2003,
  Author          = {Jankowski, J. and van der Giet, M. and Jankowski, V. and
                    Schmidt, S. and Hemeier, M. and Mahn, B. and Giebing, G.
                    and Tölle, M. and Luftmann, H. and Schlüter, H. and
                    Zidek, W. and Tepel, M.},
  Title           = {Increased plasma phenylacetic acid in patients with
                    end-stage renal failure inhibits {iNOS} expression},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2003},
  DOI             = {10.1172/jci200315524},
  Number          = {2},
  Pages           = {256--264},
  Volume          = {112}
}

@Article{Jankowski2005,
  Author          = {Jankowski, Vera and Tölle, Markus and Vanholder,
                    Raymond and Schönfelder, Gilbert and van der Giet,
                    Markus and Henning, Lars and Schlüter, Hartmut and Paul,
                    Martin and Zidek, Walter and Jankowski, Joachim},
  Title           = {Uridine adenosine tetraphosphate: {A} novel endothelium-
                    derived vasoconstrictive factor},
  JournalTitle    = {Nat. Med.},
  Date            = {2005},
  DOI             = {10.1038/nm1188},
  ids             = {jankowski2005a},
  Keywords        = {Jankowski-Selection},
  Number          = {2},
  Pages           = {223--227},
  Volume          = {11}
}

@Article{Jankowski2007,
  Author          = {Jankowski, Vera and Vanholder, Raymond and van der Giet,
                    Markus and Tölle, Markus and Karadogan, Sevil and Gobom,
                    Johan and Furkert, Jens and Oksche, Alexander and Krause,
                    Eberhard and Anh Tran, Thi Nguyet and Tepel, Martin and
                    Schuchardt, Mirjam and Schlüter, Hartmut and Wiedon,
                    Annette and Beyermann, Michael and Bader, Michael and
                    Todiras, Mihail and Zidek, Walter and Jankowski,
                    Joachim},
  Title           = {Mass-Spectrometric Identification of a Novel Angiotensin
                    Peptide in Human Plasma},
  JournalTitle    = { Arterioscl. Throm. Vas.},
  Date            = {2007},
  DOI             = {10.1161/01.atv.0000253889.09765.5f},
  Number          = {2},
  Pages           = {297--302},
  Volume          = {27}
}

@Article{Kidani2022,
  Author          = {Kidani, Yujiro and Nogami, Wataru and Yasumizu, Yoshiaki
                    and Kawashima, Atsunari and Tanaka, Atsushi and Sonoda,
                    Yudai and Tona, Yumi and Nashiki, Kunitaka and Matsumoto,
                    Reimi and Hagiwara, Masaki and Osaki, Motonao and Dohi,
                    Keiji and Kanazawa, Takayuki and Ueyama, Azumi and
                    Yoshikawa, Mai and Yoshida, Tetsuya and Matsumoto,
                    Mitsunobu and Hojo, Kanji and Shinonome, Satomi and
                    Yoshida, Hiroshi and Hirata, Michinari and Haruna, Miya
                    and Nakamura, Yamami and Motooka, Daisuke and Okuzaki,
                    Daisuke and Sugiyama, Yasuko and Kinoshita, Makoto and
                    Okuno, Tatsusada and Kato, Taigo and Hatano, Koji and
                    Uemura, Motohide and Imamura, Ryoichi and Yokoi, Kazunori
                    and Tanemura, Atsushi and Shintani, Yasushi and Kimura,
                    Tadashi and Nonomura, Norio and Wada, Hisashi and Mori,
                    Masaki and Doki, Yuichiro and Ohkura, Naganari and
                    Sakaguchi, Shimon},
  Title           = {{CCR}8-targeted specific depletion of clonally expanded
                    Treg cells in tumor tissues evokes potent tumor immunity
                    with long-lasting memory},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2022},
  DOI             = {10.1073/pnas.2114282119},
  Number          = {7},
  Volume          = {119}
}

@Article{Jankowski2007a,
  Author          = {Jankowski, V. and Karadogan, S. and Vanholder, R. and
                    Nofer, J.-R. and Herget-Rosenthal, S. and van der Giet,
                    M. and Tölle, M. and Tran, T.N.A. and Zidek, W. and
                    Jankowski, J.},
  Title           = {Paracrine stimulation of vascular smooth muscle
                    proliferation by diadenosine polyphosphates released from
                    proximal tubule epithelial cells},
  JournalTitle    = {Kidney Int.},
  Date            = {2007},
  DOI             = {10.1038/sj.ki.5002186},
  Number          = {10},
  Pages           = {994--1000},
  Volume          = {71}
}

@Article{Jankowski2011,
  Author          = {Jankowski, Vera and Tölle, Markus and Santos, Robson A.
                    S. and Günthner, Thomas and Krause, Eberhard and
                    Beyermann, Michael and Welker, Pia and Bader, Michael and
                    Pinheiro, Sergio Veloso Brant and Sampaio, Walkyria O.
                    and Lautner, Roberto and Kretschmer, Axel and Giet,
                    Markus and Zidek, Walter and Jankowski, Joachim},
  Title           = {Angioprotectin: {An} angiotensin {II‐like} peptide
                    causing vasodilatory effects},
  JournalTitle    = {The FASEB Journal},
  Date            = {2011},
  DOI             = {10.1096/fj.11-185470},
  ids             = {jankowski2011a},
  Number          = {9},
  Pages           = {2987--2995},
  Volume          = {25}
}

@Article{Jankowski2013,
  Author          = {Jankowski, Vera and Schulz, Anna and Kretschmer, Axel
                    and Mischak, Harald and Boehringer, Falko and van der
                    Giet, Markus and Janke, Doreen and Schuchardt, Mirjam and
                    Herwig, Ralf and Zidek, Walter and Jankowski, Joachim},
  Title           = {The enzymatic activity of the {VEGFR2} receptor for the
                    biosynthesis of dinucleoside polyphosphates},
  JournalTitle    = {J. Mol. Med.},
  Date            = {2013},
  DOI             = {10.1007/s00109-013-1036-y},
  Number          = {9},
  Pages           = {1095--1107},
  Volume          = {91}
}

@Article{Jankowski2021-ax,
  Author          = {Jankowski, Joachim and Floege, Jürgen and Fliser,
                    Danilo and Böhm, Michael and Marx, Nikolaus},
  Title           = {Cardiovascular Disease in Chronic Kidney Disease},
  JournalTitle    = {Circulation},
  Date            = {2021},
  DOI             = {10.1161/circulationaha.120.050686},
  Keywords        = {Jankowski-Selection},
  Number          = {11},
  Pages           = {1157--1172},
  Subtitle        = {Pathophysiological Insights and Therapeutic Options},
  Volume          = {143}
}

@Article{Jankowski2022-iy,
  Author          = {Jankowski, Vera and Saritas, Turgay and Kjolby, Mads and
                    Hermann, Juliane and Speer, Thimoteus and Himmelsbach,
                    Anika and Mahr, Kerstin and Heuschkel, Marina Augusto and
                    Schunk, Stefan J and Thirup, Soren and Winther, Simon and
                    Bottcher, Morten and Nyegard, Mette and Nykjaer, Anders
                    and Kramann, Rafael and Kaesler, Nadine and Jankowski,
                    Joachim and Floege, Juergen and Marx, Nikolaus and
                    Goettsch, Claudia},
  Title           = {Carbamylated sortilin associates with cardiovascular
                    calcification in patients with chronic kidney disease},
  JournalTitle    = {Kidney Int.},
  Date            = {2022},
  DOI             = {10.1016/j.kint.2021.10.018},
  Keywords        = {Jankowski-Selection},
  Number          = {3},
  Pages           = {574--584},
  Volume          = {101}
}

@Article{Jansen2018-wa,
  Author          = {Jansen, Christian and Möller, Philipp and Meyer,
                    Carsten and Kolbe, Carl Christian and Bogs, Christopher
                    and Pohlmann, Alessandra and Schierwagen, Robert and
                    Praktiknjo, Michael and Abdullah, Zeinab and Lehmann,
                    Jennifer and Thomas, Daniel and Strassburg, Christian P
                    and Latz, Eicke and Mueller, Sebastian and Rössle,
                    Martin and Trebicka, Jonel},
  Title           = {Increase in liver stiffness after transjugular
                    intrahepatic portosystemic shunt is associated with
                    inflammation and predicts mortality},
  JournalTitle    = {Hepatology},
  Date            = {2018},
  DOI             = {10.1002/hep.29612},
  ids             = {jansen_increase_2018},
  Keywords        = {Trebicka-Selection},
  Number          = {4},
  Pages           = {1472--1484},
  Volume          = {67}
}

@Article{Jarnagin2002-vt,
  Author          = {Jarnagin, William R. and Gonen, Mithat and Fong, Yuman
                    and DeMatteo, Ronald P. and Ben-Porat, Leah and Little,
                    Sarah and Corvera, Carlos and Weber, Sharon and Blumgart,
                    Leslie H.},
  Title           = {Improvement in perioperative outcome after hepatic
                    resection: analysis of 1,803 consecutive cases over the
                    past decade},
  JournalTitle    = {Ann. Surg.},
  Date            = {2002},
  DOI             = {10.1097/00000658-200210000-00001},
  Number          = {4},
  Pages           = {397--406,discussion 406--7},
  Volume          = {236}
}

@Article{Jones2019-ab,
  Author          = {Jones, F and Doherty, G A},
  Title           = {Vedolizumab in {IBD}/{PSC}: A Case for Careful
                    Vigilance?},
  JournalTitle    = {J. Crohns Colitis},
  Date            = {2019},
  DOI             = {10.1093/ecco-jcc/jjz102},
  Number          = {10},
  Pages           = {1237--1238},
  Volume          = {13}
}

@Article{Just:756781,
  Author          = {Just, Sarah and Mondot, Stanislas and Ecker, Josef and
                    Wegner, Katrin and Rath, Eva and Gau, Laura and Streidl,
                    Theresa and Hery-Arnaud, Genevieve and Schmidt, Sinah and
                    Lesker, Till Robin and Bieth, Valentin and Dunkel,
                    Andreas and Strowig, Till and Hofmann, Thomas and Haller,
                    Dirk and Liebisch, Gerhard and Gérard, Philippe and
                    Rohn, Sascha and Lepage, Patricia and Clavel, Thomas},
  Title           = {The gut microbiota drives the impact of bile acids and
                    fat source in diet on mouse metabolism},
  JournalTitle    = {Microbiome},
  Date            = {2018},
  DOI             = {10.1186/s40168-018-0510-8},
  Keywords        = {Clavel-Selection},
  Number          = {1},
  Pages           = {134},
  Volume          = {6}
}

@Article{Mizuno2022,
  Author          = {Mizuno, Rin and Hojo, Hiroaki and Takahashi, Masatomo
                    and Kashio, Soshiro and Enya, Sora and Nakao, Motonao and
                    Konishi, Riyo and Yoda, Mayuko and Harata, Ayano and
                    Hamanishi, Junzo and Kawamoto, Hiroshi and Mandai, Masaki
                    and Suzuki, Yutaka and Miura, Masayuki and Bamba, Takeshi
                    and Izumi, Yoshihiro and Kawaoka, Shinpei},
  Title           = {Remote solid cancers rewire hepatic nitrogen metabolism
                    via host nicotinamide-N-methyltransferase},
  JournalTitle    = {Nat. Commun.},
  Date            = {2022},
  DOI             = {10.1038/s41467-022-30926-z},
  Number          = {1},
  Volume          = {13}
}

@Article{Kabbert:794137,
  Author          = {Kabbert, Johanna and Benckert, Julia and Rollenske, Tim
                    and Hitch, Thomas C. A. and Clavel, Thomas and Cerovic,
                    Vuk and Wardemann, Hedda and Pabst, Oliver},
  Title           = {High microbiota reactivity of adult human intestinal IgA
                    requires somatic mutations},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2020},
  DOI             = {10.1084/jem.20200275},
  Keywords        = {Pabst-Selection,CRC1382-Project B03,CRC1382-Project
                    A05,CRC1382-Project Q02,CRC1382-Project
                    B06,CRC1382-Project B06,CRC1382-Project Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {11},
  Pages           = {e20200275},
  ShortJournal    = {JEM},
  Volume          = {217}
}

@Article{Kakiyama2013Modulation,
  Author          = {Kakiyama, Genta and Pandak, William M. and Gillevet,
                    Patrick M. and Hylemon, Phillip B. and Heuman, Douglas M.
                    and Daita, Kalyani and Takei, Hajime and Muto, Akina and
                    Nittono, Hiroshi and Ridlon, Jason M. and White, Melanie
                    B. and Noble, Nicole A. and Monteith, Pamela and Fuchs,
                    Michael and Thacker, Leroy R. and Sikaroodi, Masoumeh and
                    Bajaj, Jasmohan S.},
  Title           = {Modulation of the fecal bile acid profile by gut
                    microbiota in cirrhosis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2013-05},
  DOI             = {10.1016/j.jhep.2013.01.003},
  Number          = {5},
  Pages           = {949--955},
  Volume          = {58}
}

@Article{Katsiki2016-lh,
  Author          = {Katsiki, Niki and Mikhailidis, Dimitri P. and Mantzoros,
                    Christos S.},
  Title           = {Non-alcoholic fatty liver disease and dyslipidemia: {An}
                    update},
  JournalTitle    = {Metabolis.},
  Date            = {2016},
  DOI             = {10.1016/j.metabol.2016.05.003},
  Keywords        = {Antidiabetic drugs; Dyslipidemia; Ezetimibe;
                    Non-alcoholic fatty liver disease; Statins},
  Number          = {8},
  Pages           = {1109--1123},
  Volume          = {65}
}

@Article{Kazankov2019-hu,
  Author          = {Kazankov, Konstantin and Jørgensen, Simon Mark Dahl and
                    Thomsen, Karen Louise and Møller, Holger Jon and
                    Vilstrup, Hendrik and George, Jacob and Schuppan, Detlef
                    and Grønbæk, Henning},
  Title           = {The role of macrophages in nonalcoholic fatty liver
                    disease and nonalcoholic steatohepatitis},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2018},
  DOI             = {10.1038/s41575-018-0082-x},
  Number          = {3},
  Pages           = {145--159},
  Volume          = {16}
}

@Article{Kbeck2016,
  Author          = {Kübeck, Raphaela and Bonet-Ripoll, Catalina and
                    Hoffmann, Christina and Walker, Alesia and Müller,
                    Veronika Maria and Schüppel, Valentina Luise and
                    Lagkouvardos, Ilias and Scholz, Birgit and Engel,
                    Karl-Heinz and Daniel, Hannelore and Schmitt-Kopplin,
                    Philippe and Haller, Dirk and Clavel, Thomas and
                    Klingenspor, Martin},
  Title           = {Dietary fat and gut microbiota interactions determine
                    diet-induced obesity in mice},
  JournalTitle    = {Mol. Metab.},
  Date            = {2016},
  DOI             = {10.1016/j.molmet.2016.10.001},
  Number          = {12},
  Pages           = {1162--1174},
  Volume          = {5}
}

@Article{Di_Ruscio2017-bd,
  Author          = {Di Ruscio, Mirko and Vernia, Filippo and Ciccone,
                    Antonio and Frieri, Giuseppe and Latella, Giovanni},
  Title           = {Surrogate fecal biomarkers in inflammatory bowel
                    disease: Rivals or complementary tools of fecal
                    calprotectin?},
  JournalTitle    = {Inflamm. Bowel Dis.},
  Date            = {2017},
  DOI             = {10.1093/ibd/izx011},
  Keywords        = {Crohn's disease; IBD; fecal markers; ulcerative
                    colitis},
  Number          = {1},
  Pages           = {78--92},
  Volume          = {24}
}

@Article{Patel2022-qk,
  Author          = {Patel, Vishal C. and Lee, Sunjae and McPhail, Mark J.W.
                    and Da Silva, Kevin and Guilly, Susie and Zamalloa, Ane
                    and Witherden, Elizabeth and Støy, Sidsel and Manakkat
                    Vijay, Godhev Kumar and Pons, Nicolas and Galleron,
                    Nathalie and Huang, Xaiohong and Gencer, Selin and Coen,
                    Muireann and Tranah, Thomas Henry and Wendon, Julia
                    Alexis and Bruce, Kenneth D. and Le Chatelier, Emmanuelle
                    and Ehrlich, Stanislav Dusko and Edwards, Lindsey Ann and
                    Shoaie, Saeed and Shawcross, Debbie Lindsay},
  Title           = {Rifaximin-α reduces gut-derived inflammation and mucin
                    degradation in cirrhosis and encephalopathy: {Rifsys}
                    randomised controlled trial},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2021.09.010},
  Keywords        = {Hepatic encephalopathy; cirrhosis; gut microbiome;
                    rifaximin-α; salivary microbiome; systemic
                    inflammation},
  Number          = {2},
  Pages           = {332--342},
  Volume          = {76}
}

@Article{Muller2018-lr,
  Author          = {Muller, Florian and Schug, David and Hallen, Patrick and
                    Grahe, Jan and Schulz, Volkmar},
  Title           = {Gradient Tree Boosting-Based Positioning Method for
                    Monolithic Scintillator Crystals in Positron Emission
                    Tomography},
  JournalTitle    = {IEEE Trans. Radiat. Plasma Med. Sci.},
  Date            = {2018},
  DOI             = {10.1109/trpms.2018.2837738},
  Number          = {5},
  Pages           = {411--421},
  Volume          = {2}
}

@Article{Ke2019-fs,
  Author          = {Ke, Xinxin and Walker, Alesia and Haange, Sven-Bastiaan
                    and Lagkouvardos, Ilias and Liu, Yuwen and
                    Schmitt-Kopplin, Philippe and von Bergen, Martin and
                    Jehmlich, Nico and He, Xin and Clavel, Thomas and Cheung,
                    Peter C K},
  Title           = {Synbiotic-driven improvement of metabolic disturbances
                    is associated with changes in the gut microbiome in
                    diet-induced obese mice},
  JournalTitle    = {Mol. Metab.},
  Date            = {2019},
  DOI             = {10.1016/j.molmet.2019.01.012},
  Keywords        = {Dietary intervention; Gut microbiota; High-fat diet;
                    Obesity; Synbiotics},
  Pages           = {96--109},
  Volume          = {22}
}

@Article{El-Khoueiry2017-jk,
  Author          = {El-Khoueiry, Anthony B and Sangro, Bruno and Yau, Thomas
                    and Crocenzi, Todd S and Kudo, Masatoshi and Hsu, Chiun
                    and Kim, Tae-You and Choo, Su-Pin and Trojan, Jörg and
                    Welling, Rd, Theodore H and Meyer, Tim and Kang, Yoon-Koo
                    and Yeo, Winnie and Chopra, Akhil and Anderson, Jeffrey
                    and Dela Cruz, Christine and Lang, Lixin and Neely,
                    Jaclyn and Tang, Hao and Dastani, Homa B and Melero,
                    Ignacio},
  Title           = {Nivolumab in patients with advanced hepatocellular
                    carcinoma {({CheckMate}} 040): {An} open-label,
                    non-comparative, phase 1/2 dose escalation and expansion
                    trial},
  JournalTitle    = {Lancet},
  Date            = {2017},
  DOI             = {10.1016/S0140-6736(17)31046-2},
  Number          = {10088},
  Pages           = {2492--2502},
  Volume          = {389}
}

@Article{Khan2019-jg,
  Author          = {Khan, Omar and Giles, Josephine R. and McDonald, Sierra
                    and Manne, Sasikanth and Ngiow, Shin Foong and Patel,
                    Kunal P. and Werner, Michael T. and Huang, Alexander C.
                    and Alexander, Katherine A. and Wu, Jennifer E. and
                    Attanasio, John and Yan, Patrick and George, Sangeeth M.
                    and Bengsch, Bertram and Staupe, Ryan P. and Donahue,
                    Greg and Xu, Wei and Amaravadi, Ravi K. and Xu, Xiaowei
                    and Karakousis, Giorgos C. and Mitchell, Tara C. and
                    Schuchter, Lynn M. and Kaye, Jonathan and Berger, Shelley
                    L. and Wherry, E. John},
  Title           = {{TOX} transcriptionally and epigenetically programs
                    {CD8+} T cell exhaustion},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-019-1325-x},
  Number          = {7764},
  Pages           = {211--218},
  Volume          = {571}
}

@Article{Kieling:133948,
  Author          = {Kiessling, Fabian and Huppert, Jochen and Zhang, Chunfu
                    and Jayapaul, Jabadurai and Zwick, Stefan and Woenne, Eva
                    C. and Mueller, Margareta M. and Zentgraf, Hanswalter and
                    Eisenhut, Michael and Addadi, Yoseph and Neeman, Michal
                    and Semmler, Wolfhard},
  Title           = {{RGD}-labeled {USPIO} Inhibits Adhesion and Endocytotic
                    Activity of αvβ3-Integrin–expressing Glioma Cells and
                    Only Accumulates in the Vascular Tumor Compartment},
  JournalTitle    = {Radiology},
  Date            = {2009},
  DOI             = {10.1148/radiol.2532081815},
  Number          = {2},
  Pages           = {462--469},
  Volume          = {253}
}

@Article{Deczkowska2021-mi,
  Author          = {Deczkowska, Aleksandra and David, Eyal and Ramadori,
                    Pierluigi and Pfister, Dominik and Safran, Michal and Li,
                    Baoguo and Giladi, Amir and Jaitin, Diego Adhemar and
                    Barboy, Oren and Cohen, Merav and Yofe, Ido and Gur,
                    Chamutal and Shlomi-Loubaton, Shir and Henri, Sandrine
                    and Suhail, Yousuf and Qiu, Mengjie and Kam, Shing and
                    Hermon, Hila and Lahat, Eylon and Ben Yakov, Gil and
                    Cohen-Ezra, Oranit and Davidov, Yana and Likhter, Mariya
                    and Goitein, David and Roth, Susanne and Weber, Achim and
                    Malissen, Bernard and Weiner, Assaf and Ben-Ari, Ziv and
                    Heikenwälder, Mathias and Elinav, Eran and Amit, Ido},
  Title           = {{XCR1+} type 1 conventional dendritic cells drive liver
                    pathology in non-alcoholic steatohepatitis},
  JournalTitle    = {Nat. Med.},
  Date            = {2021},
  DOI             = {10.1038/s41591-021-01344-3},
  Number          = {6},
  Pages           = {1043--1054},
  Volume          = {27}
}

@Article{Wiggins2022-yt,
  Author          = {Wiggins, Benjamin G and Pallett, Laura J and Li, Xiaoyan
                    and Davies, Scott P and Amin, Oliver E and Gill, Upkar S
                    and Kucykowicz, Stephanie and Patel, Arzoo M and Aliazis,
                    Konstantinos and Liu, Yuxin S and Reynolds, Gary M and
                    Davidson, Brian R and Gander, Amir and Luong, Tu Vinh and
                    Hirschfield, Gideon M and Kennedy, Patrick T F and Huang,
                    Yuehua and Maini, Mala K and Stamataki, Zania},
  Title           = {The human liver microenvironment shapes the homing and
                    function of {CD4\textsuperscript{+}} T-cell populations},
  JournalTitle    = {Gut},
  Date            = {2021},
  DOI             = {10.1136/gutjnl-2020-323771},
  Keywords        = {T lymphocytes; cellular immunity; hepatitis B;
                    immunology; liver immunology},
  Number          = {7},
  Pages           = {1399--1411},
  Volume          = {71}
}

@Article{Volckmar2017-ua,
  Author          = {Volckmar, Julia and Gereke, Marcus and Ebensen, Thomas
                    and Riese, Peggy and Philipsen, Lars and Lienenklaus,
                    Stefan and Wohlleber, Dirk and Klopfleisch, Robert and
                    Stegemann-Koniszewski, Sabine and Müller, Andreas J. and
                    Gruber, Achim D. and Knolle, Percy and Guzman, Carlos A.
                    and Bruder, Dunja},
  Title           = {Targeted antigen delivery to dendritic cells elicits
                    robust antiviral T cell-mediated immunity in the liver},
  JournalTitle    = {Sci. Rep.},
  Date            = {2017},
  DOI             = {10.1038/srep43985},
  Number          = {1},
  Pages           = {43985},
  Volume          = {7}
}

@Article{Kiessling2004X,
  Author          = {Kiessling, Fabian and Greschus, Susanne and Lichy,
                    Matthias P and Bock, Michael and Fink, Christian and
                    Vosseler, Silvia and Moll, Jens and Mueller, Margareta M
                    and Fusenig, Norbert E. and Traupe, Horst and Semmler,
                    Wolfhard},
  Title           = {Volumetric computed tomography {(VCT):} {A} new
                    technology for noninvasive, high-resolution monitoring of
                    tumor angiogenesis},
  JournalTitle    = {Nat. Med.},
  Date            = {2004},
  DOI             = {10.1038/nm1101},
  Keywords        = {Kießling-Selection},
  Number          = {10},
  Pages           = {1133--1138},
  Volume          = {10}
}

@Article{Narsale2014,
  Author          = {Narsale, Aditi A. and Carson, James A.},
  Title           = {Role of interleukin-6 in cachexia},
  JournalTitle    = {Curr. Opin. Supportive and Palliative Care},
  Date            = {2014},
  DOI             = {10.1097/spc.0000000000000091},
  Number          = {4},
  Pages           = {321--327},
  Volume          = {8}
}

@Article{Kindt:756779,
  Author          = {Kindt, Alida and Liebisch, Gerhard and Clavel, Thomas
                    and Haller, Dirk and Hörmannsperger, Gabriele and Yoon,
                    Hongsup and Kolmeder, Daniela and Sigruener, Alexander
                    and Krautbauer, Sabrina and Seeliger, Claudine and
                    Ganzha, Alexandra and Schweizer, Sabine and Morisset,
                    Rosalie and Strowig, Till and Daniel, Hannelore and Helm,
                    Dominic and Küster, Bernhard and Krumsiek, Jan and
                    Ecker, Josef},
  Title           = {The gut microbiota promotes hepatic fatty acid
                    desaturation and elongation in mice},
  JournalTitle    = {Nat. Commun.},
  Date            = {2018},
  DOI             = {10.1038/s41467-018-05767-4},
  Number          = {1},
  Pages           = {3760},
  Volume          = {9}
}

@Article{Kleemann2007-bd,
  Author          = {Kleemann, Robert and Verschuren, Lars and van Erk,
                    Marjan J and Nikolsky, Yuri and Cnubben, Nicole H P and
                    Verheij, Elwin R and Smilde, Age K and Hendriks, Henk F J
                    and Zadelaar, Susanne and Smith, Graham J and Kaznacheev,
                    Valery and Nikolskaya, Tatiana and Melnikov, Anton and
                    Hurt-Camejo, Eva and van der Greef, Jan and van Ommen,
                    Ben and Kooistra, Teake},
  Title           = {Atherosclerosis and liver inflammation induced by
                    increased dietary cholesterol intake: a combined
                    transcriptomics and metabolomics analysis},
  JournalTitle    = {Genome Biol.},
  Date            = {2007},
  DOI             = {10.1186/gb-2007-8-9-r200},
  Number          = {9},
  Pages           = {R200},
  Volume          = {8}
}

@Article{Klein2012,
  Author          = {Klein, Sabine and Van Beuge, Marike Marjolijn and
                    Granzow, Michaela and Beljaars, Leonie and Schierwagen,
                    Robert and Kilic, Sibel and Heidari, Iren and Huss,
                    Sebastian and Sauerbruch, Tilman and Poelstra, Klaas and
                    Trebicka, Jonel},
  Title           = {{HSC}-specific inhibition of Rho-kinase reduces portal
                    pressure in cirrhotic rats without major systemic
                    effects},
  JournalTitle    = {J. Hepatol.},
  Date            = {2012},
  DOI             = {10.1016/j.jhep.2012.07.033},
  Number          = {6},
  Pages           = {1220--1227},
  Volume          = {57}
}

@Article{Klein2015,
  Author          = {Klein, Sabine and Rick, Johanna and Lehmann, Jennifer
                    and Schierwagen, Robert and Schierwagen, Irela Gretchen
                    and Verbeke, Len and Hittatiya, Kanishka and Uschner,
                    Frank Erhard and Manekeller, Steffen and Strassburg,
                    Christian P and Wagner, Kay-Uwe and Sayeski, Peter P and
                    Wolf, Dominik and Laleman, Wim and Sauerbruch, Tilman and
                    Trebicka, Jonel},
  Title           = {{Janus}-kinase-2 relates directly to portal hypertension
                    and to complications in rodent and human cirrhosis},
  JournalTitle    = {Gut},
  Date            = {2015},
  DOI             = {10.1136/gutjnl-2015-309600},
  ids             = {klein2017a},
  Number          = {1},
  Pages           = {145--155},
  Volume          = {66}
}

@Article{Klein:791931,
  Author          = {Klein, Leah Maria and Chang, Johannes and Gu, Wenyi and
                    Manekeller, Steffen and Jansen, Christian and Lingohr,
                    Philipp and Praktiknjo, Michael and Kalf, Jörg C. and
                    Schulz, Martin and Spengler, Ulrich and Strassburg,
                    Christian and Cárdenas, Andrés and Arroyo, Vicente and
                    Trebicka, Jonel},
  Title           = {The Development and Outcome of Acute-on-Chronic Liver
                    Failure After Surgical Interventions},
  JournalTitle    = {Liver Transplant.},
  Date            = {2020},
  DOI             = {10.1002/lt.25675},
  Keywords        = {,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {227--237},
  Volume          = {26}
}

@Article{Kleinjans:852859,
  Author          = {Kleinjans, Moritz and Schneider, Carolin Victoria and
                    Bruns, Tony and Strnad, Pavel},
  Title           = {Phenome of coeliac disease vs. inflammatory bowel
                    disease},
  JournalTitle    = {Sci. Rep.},
  Date            = {2022},
  DOI             = {10.1038/s41598-022-18593-y},
  Keywords        = {,CRC1382-Project B07,CRC1382-Project A03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {14572},
  Volume          = {12}
}

@Article{Kociubinski2002-rx,
  Author          = {Kociubinski, Guillermo and Zavaglia, Andrea Gómez and
                    Pérez, Pablo F and Disalvo, Edgardo A and De Antoni,
                    Graciela L},
  Title           = {Effect of bile components on the surface properties of
                    bifidobacteria},
  JournalTitle    = {J. Dairy Res.},
  Date            = {2002},
  DOI             = {10.1017/s0022029901005313},
  Number          = {2},
  Pages           = {293--302},
  Volume          = {69}
}

@Article{Koelfat2019-nx,
  Author          = {Koelfat, Kiran V.K. and Plummer, Mark P. and Schaap,
                    Frank G. and Lenicek, Martin and Jansen, Peter L.M. and
                    Deane, Adam M. and Olde Damink, Steven W.M.},
  Title           = {Gallbladder Dyskinesia Is Associated With an Impaired
                    Postprandial Fibroblast Growth Factor 19 Response in
                    Critically Ill Patients},
  JournalTitle    = {Hepatology},
  Date            = {2019},
  DOI             = {10.1002/hep.30629},
  Keywords        = {Schaap-Selection},
  Number          = {1},
  Pages           = {308--318},
  Volume          = {70}
}

@Article{Koelfat2021-hf,
  Author          = {Koelfat, Kiran V.K. and Mierlo, Kim M.C. and Lodewick,
                    Toine M. and Bloemen, Johanne G. and Kroft, Gregory and
                    Amygdalos, Iakovos and Neumann, Ulf P. and Dejong,
                    Cornelis H.C. and Jansen, Peter L.M. and Olde Damink,
                    Steven W.M. and Schaap, Frank G.},
  Title           = {Bile Salt and {FGF19} Signaling in the Early Phase of
                    Human Liver Regeneration},
  JournalTitle    = {Hepatology Communications},
  Date            = {2021},
  DOI             = {10.1002/hep4.1728},
  Keywords        = {Olde Damink-Selection,Schaap-Selection},
  Number          = {8},
  Pages           = {1400--1411},
  Volume          = {5}
}

@Article{Koelfat2021-jb,
  Author          = {Koelfat, Kiran V K and Picot, Denis and Chang, Xinwei
                    and Desille-Dugast, Mireille and van Eijk, Hans M and van
                    Kuijk, Sander M J and Lenicek, Martin and Layec, Sabrina
                    and Carsin, Marie and Dussaulx, Laurence and Seynhaeve,
                    Eloi and Trivin, Florence and Lacaze, Laurence and
                    Thibault, Ronan and Schaap, Frank G and Olde Damink,
                    Steven W M},
  Title           = {Chyme reinfusion restores the regulatory bile
                    {salt-FGF19} axis in patients with intestinal failure},
  JournalTitle    = {Hepatology},
  Date            = {2021},
  Addendum        = sharedlast,
  author+an:default = {14=sharedLast;15=sharedLast;16=sharedLast},
  DOI             = {10.1002/hep.32017},
  Keywords        = {Olde Damink-Selection,Schaap-Selection},
  Number          = {5},
  Pages           = {2670--2683},
  Volume          = {74}
}

@Article{Koenen2022-by,
  Author          = {Koenen, Maria Teresa and Brandt, Elisa Fabiana and
                    Kaczor, Dawid Marcin and Caspers, Tim and Heinzmann,
                    Alexandra Catharina Anna and Fischer, Petra and
                    Heinrichs, Daniel and Wirtz, Theresa Hildegard and
                    Trautwein, Christian and Koenen, Rory R and Berres,
                    Marie-Luise},
  Title           = {Extracellular vesicles from steatotic hepatocytes
                    provoke pro-fibrotic responses in cultured stellate
                    cells},
  JournalTitle    = {Biomolecules},
  Addendum        = preliminarywork,
  Date            = {2022},
  DOI             = {10.3390/biom12050698},
  ids             = {Koenen2022-qv},
  Keywords        = {Berres-Selection},
  Number          = {5},
  Pages           = {698},
  Volume          = {12}
}

@Article{Kolyva2021-tb,
  Author          = {Kolyva, Soultana and Triga, Maria and Kritikou, Dimitra
                    and Chrysis, Dionisios},
  Title           = {The effect of feeding patterns on serum zonulin levels
                    in infants at 3–4 months of age},
  JournalTitle    = {Eur. J. Pediatr.},
  Date            = {2021},
  DOI             = {10.1007/s00431-021-04102-2},
  Keywords        = {Breastfeeding; Formula feeding; Gut closure; Intestinal
                    permeability; Zonulin},
  Number          = {11},
  Pages           = {3273--3278},
  Volume          = {180}
}

@Article{Kootte2017,
  Author          = {Kootte, Ruud S. and Levin, Evgeni and Salojärvi, Jarkko
                    and Smits, Loek P. and Hartstra, Annick V. and Udayappan,
                    Shanti D. and Hermes, Gerben and Bouter, Kristien E. and
                    Koopen, Annefleur M. and Holst, Jens J. and Knop, Filip
                    K. and Blaak, Ellen E. and Zhao, Jing and Smidt, Hauke
                    and Harms, Amy C. and Hankemeijer, Thomas and Bergman,
                    Jacques J.G.H.M. and Romijn, Hans A. and Schaap, Frank G.
                    and Olde Damink, Steven W.M. and Ackermans, Mariette T.
                    and Dallinga-Thie, Geesje M. and Zoetendal, Erwin and de
                    Vos, Willem M. and Serlie, Mireille J. and Stroes, Erik
                    S.G. and Groen, Albert K. and Nieuwdorp, Max},
  Title           = {Improvement of Insulin Sensitivity after Lean Donor
                    Feces in Metabolic Syndrome Is Driven by Baseline
                    Intestinal Microbiota Composition},
  JournalTitle    = {Cell Metab.},
  Date            = {2017},
  DOI             = {10.1016/j.cmet.2017.09.008},
  Number          = {4},
  Pages           = {611--619.e6},
  Volume          = {26}
}

@Article{Koumakis2019-dp,
  Author          = {Koumakis, Eugénie and Millet-Botti, Joëlle and Benna,
                    Jamel El and Leroy, Christine and Boitez, Valérie and
                    Codogno, Patrice and Friedlander, Gérard and Forand,
                    Anne},
  Title           = {Novel function of {PiT1/SLC20A1} in {LPS-related}
                    inflammation and wound healing},
  JournalTitle    = {Sci. Rep.},
  Date            = {2019},
  DOI             = {10.1038/s41598-018-37551-1},
  Number          = {1},
  Pages           = {1808},
  Volume          = {9}
}

@Article{Kpfer:196183,
  Author          = {Kuepfer, Lars and Sauer, Uwe and Blank, Lars M.},
  Title           = {Metabolic functions of duplicate genes in Saccharomyces
                    cerevisiae},
  JournalTitle    = {Genome Res.},
  Date            = {2005},
  DOI             = {10.1101/gr.3992505},
  Keywords        = {Blank-Selection},
  Number          = {10},
  Pages           = {1421--1430},
  Volume          = {15}
}

@Article{Krenkel2020-nr,
  Author          = {Krenkel, Oliver and Hundertmark, Jana and Abdallah, Ali
                    T and Kohlhepp, Marlene and Puengel, Tobias and Roth,
                    Tilmann and Branco, Diogo Philippini Pontual and
                    Mossanen, Jana C and Luedde, Tom and Trautwein, Christian
                    and Costa, Ivan G and Tacke, Frank},
  Title           = {Myeloid cells in liver and bone marrow acquire a
                    functionally distinct inflammatory phenotype during
                    obesity-related steatohepatitis},
  JournalTitle    = {Gut},
  Addendum        = preliminarywork,
  Date            = {2020},
  DOI             = {10.1136/gutjnl-2019-318382},
  Keywords        = {Tacke-Selection},
  Number          = {3},
  Pages           = {551--563},
  Volume          = {69}
}

@Article{Krenkel:706913,
  Author          = {Krenkel, Oliver and Puengel, Tobias and Govaere, Olivier
                    and Abdallah, Ali T. and Mossanen, Jana C. and Kohlhepp,
                    Marlene and Liepelt, Anke and Lefebvre, Eric and Luedde,
                    Tom and Hellerbrand, Claus and Weiskirchen, Ralf and
                    Longerich, Thomas and Costa, Ivan G. and Anstee, Quentin
                    M. and Trautwein, Christian and Tacke, Frank},
  Title           = {Therapeutic inhibition of inflammatory monocyte
                    recruitment reduces steatohepatitis and liver fibrosis},
  JournalTitle    = {Hepatology},
  Date            = {2018},
  DOI             = {10.1002/hep.29544},
  Keywords        = {Tacke-Selection},
  Number          = {4},
  Pages           = {1270--1283},
  Subtitle        = {Metabolic Liver Disease},
  Volume          = {67}
}

@Article{Krenkel:716717,
  Author          = {Krenkel, Oliver and Tacke, Frank},
  Title           = {Liver macrophages in tissue homeostasis and disease},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2017},
  DOI             = {10.1038/nri.2017.11},
  ids             = {krenkel2017a},
  Keywords        = {Tacke-Selection},
  Number          = {5},
  Pages           = {306--321},
  Volume          = {17}
}

@Article{Kroy:446915,
  Author          = {Kroy, Daniela C. and Schumacher, Fabienne and Ramadori,
                    Pierluigi and Hatting, Maximilian and Bergheim, Ina and
                    Gassler, Nikolaus and Boekschoten, Mark V. and Müller,
                    Michael and Streetz, Konrad L. and Trautwein, Christian},
  Title           = {Hepatocyte specific deletion of c-Met leads to the
                    development of severe non-alcoholic steatohepatitis in
                    mice},
  JournalTitle    = {J. Hepatol.},
  Date            = {2014},
  DOI             = {10.1016/j.jhep.2014.05.019},
  Keywords        = {Hatting-Selection},
  Number          = {4},
  Pages           = {883--890},
  Volume          = {61}
}

@Article{Kucukoglu:445575,
  Author          = {Kucukoglu, Ozlem and Guldiken, Nurdan and Chen, Yu and
                    Usachov, Valentyn and El-Heliebi, Amin and Haybaeck,
                    Johannes and Denk, Helmut and Trautwein, Christian and
                    Strnad, Pavel},
  Title           = {High-fat diet triggers {Mallory}-Denk body formation
                    through misfolding and crosslinking of excess keratin 8},
  JournalTitle    = {Hepatology},
  Date            = {2014},
  DOI             = {10.1002/hep.27068},
  Number          = {1},
  Pages           = {169--178},
  Subtitle        = {KUCUKOGLU ET AL.},
  Volume          = {60}
}

@Article{Pfister2021,
  Author          = {Pfister, Dominik and Núñez, Nicolás Gonzalo and
                    Pinyol, Roser and Govaere, Olivier and Pinter, Matthias
                    and Szydlowska, Marta and Gupta, Revant and Qiu, Mengjie
                    and Deczkowska, Aleksandra and Weiner, Assaf and Müller,
                    Florian and Sinha, Ankit and Friebel, Ekaterina and
                    Engleitner, Thomas and Lenggenhager, Daniela and Moncsek,
                    Anja and Heide, Danijela and Stirm, Kristin and Kosla,
                    Jan and Kotsiliti, Eleni and Leone, Valentina and Dudek,
                    Michael and Yousuf, Suhail and Inverso, Donato and Singh,
                    Indrabahadur and Teijeiro, Ana and Castet, Florian and
                    Montironi, Carla and Haber, Philipp K. and Tiniakos, Dina
                    and Bedossa, Pierre and Cockell, Simon and Younes, Ramy
                    and Vacca, Michele and Marra, Fabio and Schattenberg,
                    Jörn M. and Allison, Michael and Bugianesi, Elisabetta
                    and Ratziu, Vlad and Pressiani, Tiziana and D'Alessio,
                    Antonio and Personeni, Nicola and Rimassa, Lorenza and
                    Daly, Ann K. and Scheiner, Bernhard and Pomej, Katharina
                    and Kirstein, Martha M. and Vogel, Arndt and
                    Peck-Radosavljevic, Markus and Hucke, Florian and
                    Finkelmeier, Fabian and Waidmann, Oliver and Trojan,
                    Jörg and Schulze, Kornelius and Wege, Henning and Koch,
                    Sandra and Weinmann, Arndt and Bueter, Marco and
                    Rössler, Fabian and Siebenhüner, Alexander and Dosso,
                    Sara De and Mallm, Jan-Philipp and Umansky, Viktor and
                    Jugold, Manfred and Luedde, Tom and Schietinger, Andrea
                    and Schirmacher, Peter and Emu, Brinda and Augustin,
                    Hellmut G. and Billeter, Adrian and Müller-Stich, Beat
                    and Kikuchi, Hiroto and Duda, Dan G. and Kütting, Fabian
                    and Waldschmidt, Dirk-Thomas and Ebert, Matthias Philip
                    and Rahbari, Nuh and Mei, Henrik E. and Schulz, Axel
                    Ronald and Ringelhan, Marc and Malek, Nisar and Spahn,
                    Stephan and Bitzer, Michael and de Galarreta, Marina Ruiz
                    and Lujambio, Amaia and Dufour, Jean-Francois and Marron,
                    Thomas U. and Kaseb, Ahmed and Kudo, Masatoshi and Huang,
                    Yi-Hsiang and Djouder, Nabil and Wolter, Katharina and
                    Zender, Lars and Marche, Parice N. and Decaens, Thomas
                    and Pinato, David J. and Rad, Roland and Mertens, Joachim
                    C. and Weber, Achim and Unger, Kristian and Meissner,
                    Felix and Roth, Susanne and Jilkova, Zuzana Macek and
                    Claassen, Manfred and Anstee, Quentin M. and Amit, Ido
                    and Knolle, Percy and Becher, Burkhard and Llovet, Josep
                    M. and Heikenwalder, Mathias},
  Title           = {{NASH} limits anti-tumour surveillance in
                    immunotherapy-treated {HCC}},
  JournalTitle    = {Nature},
  Date            = {2021},
  DOI             = {10.1038/s41586-021-03362-0},
  Number          = {7854},
  Pages           = {450--456},
  Volume          = {592}
}

@Article{Kuhl2005,
  Author          = {Kuhl, Christiane K. and Schrading, Simone and Leutner,
                    Claudia C. and Morakkabati-Spitz, Nuschin and Wardelmann,
                    Eva and Fimmers, Rolf and Kuhn, Walther and Schild, Hans
                    H.},
  Title           = {Mammography, Breast Ultrasound, and Magnetic Resonance
                    Imaging for Surveillance of Women at High Familial Risk
                    for Breast Cancer},
  JournalTitle    = {J. Clin. Oncol.},
  Date            = {2005},
  DOI             = {10.1200/jco.2004.00.4960},
  Keywords        = {Kuhl-Selection},
  Number          = {33},
  Pages           = {8469--8476},
  Volume          = {23}
}

@Article{Kuhl2007,
  Author          = {Kuhl, Christiane K and Schrading, Simone and Bieling,
                    Heribert B and Wardelmann, Eva and Leutner, Claudia C and
                    Koenig, Roy and Kuhn, Walther and Schild, Hans H},
  Title           = {{MRI} for diagnosis of pure ductal carcinoma in situ:
                    {A} prospective observational study},
  JournalTitle    = {The Lancet},
  Date            = {2007},
  DOI             = {10.1016/s0140-6736(07)61232-x},
  Keywords        = {Kuhl-Selection},
  Number          = {9586},
  Pages           = {485--492},
  Volume          = {370}
}

@Article{Kuhl2008,
  Author          = {Kuhl, Christiane K.},
  Title           = {The {“Coming} of Age” of Nonmammographic Screening
                    for Breast Cancer},
  JournalTitle    = {JAMA},
  Date            = {2008},
  DOI             = {10.1001/jama.299.18.2203},
  Keywords        = {Kuhl-Selection},
  Number          = {18},
  Pages           = {2203},
  Volume          = {299}
}

@Article{Kuhl2019,
  Author          = {Kuhl, Christiane K. and Alparslan, Yunus and Schmoee,
                    Jonas and Sequeira, Bruno and Keulers, Annika and
                    Brümmendorf, Tim H. and Keil, Sebastian},
  Title           = {Validity of {RECIST} Version 1.1 for Response Assessment
                    in Metastatic Cancer: {A} Prospective, Multireader
                    Study},
  JournalTitle    = {Radiology},
  Date            = {2019},
  DOI             = {10.1148/radiol.2018180648},
  Keywords        = {Kuhl-Selection},
  Number          = {2},
  Pages           = {349--356},
  Volume          = {290}
}

@Article{Rahman2016,
  Author          = {Rahman, Khalidur and Desai, Chirayu and Iyer, Smita S.
                    and Thorn, Natalie E. and Kumar, Pradeep and Liu, Yunshan
                    and Smith, Tekla and Neish, Andrew S. and Li, Hongliang
                    and Tan, Shiyun and Wu, Pengbo and Liu, Xiaoxiong and Yu,
                    Yuanjie and Farris, Alton B. and Nusrat, Asma and Parkos,
                    Charles A. and Anania, Frank A.},
  Title           = {Loss of Junctional Adhesion Molecule A Promotes Severe
                    Steatohepatitis in Mice on a Diet High in Saturated Fat,
                    Fructose, and Cholesterol},
  JournalTitle    = {Gastroenterology},
  Date            = {2016},
  DOI             = {10.1053/j.gastro.2016.06.022},
  Number          = {4},
  Pages           = {733--746.e12},
  Volume          = {151}
}

@Article{Kuhl:196140,
  Author          = {Kuhl, Christiane and Weigel, Stefanie and Schrading,
                    Simone and Arand, Birke and Bieling, Heribert and König,
                    Roy and Tombach, Bernd and Leutner, Claudia and
                    Rieber-Brambs, Andrea and Nordhoff, Dennis and Heindel,
                    Walter and Reiser, Maximilian and Schild, Hans H.},
  Title           = {Prospective Multicenter Cohort Study to Refine
                    Management Recommendations for Women at Elevated Familial
                    Risk of Breast Cancer: {The} {EVA} Trial},
  JournalTitle    = {J. Clin. Oncol.},
  Date            = {2010},
  DOI             = {10.1200/jco.2009.23.0839},
  Keywords        = {Kuhl-Selection},
  Number          = {9},
  Pages           = {1450--1457},
  ShortJournal    = {JCO},
  Subtitle        = {The EVA trial},
  Volume          = {28}
}

@Article{Finn2020-mw,
  Author          = {Finn, Richard S. and Qin, Shukui and Ikeda, Masafumi and
                    Galle, Peter R. and Ducreux, Michel and Kim, Tae-You and
                    Kudo, Masatoshi and Breder, Valeriy and Merle, Philippe
                    and Kaseb, Ahmed O. and Li, Daneng and Verret, Wendy and
                    Xu, Derek-Zhen and Hernandez, Sairy and Liu, Juan and
                    Huang, Chen and Mulla, Sohail and Wang, Yulei and Lim, Ho
                    Yeong and Zhu, Andrew X. and Cheng, Ann-Lii},
  Title           = {Atezolizumab plus Bevacizumab in Unresectable
                    Hepatocellular Carcinoma},
  JournalTitle    = {N. Engl. J. Med.},
  Date            = {2020},
  DOI             = {10.1056/nejmoa1915745},
  Number          = {20},
  Pages           = {1894--1905},
  Volume          = {382}
}

@Article{Ichikawa2012-ie,
  Author          = {Ichikawa, Riko and Takayama, Tetsuro and Yoneno, Kazuaki
                    and Kamada, Nobuhiko and Kitazume, Mina T. and Higuchi,
                    Hajime and Matsuoka, Katsuyoshi and Watanabe, Mitsuhiro
                    and Itoh, Hiroshi and Kanai, Takanori and Hisamatsu,
                    Tadakazu and Hibi, Toshifumi},
  Title           = {Bile acids induce monocyte differentiation toward
                    interleukin-12 hypo-producing dendritic cells via a
                    {TGR5}-dependent pathway},
  JournalTitle    = {Immunology},
  Date            = {2012},
  DOI             = {10.1111/j.1365-2567.2012.03554.x},
  Number          = {2},
  Pages           = {153--162},
  Subtitle        = {Bile acids regulate dendritic cell differentiation},
  Volume          = {136}
}

@Article{Kuhl:446056,
  Author          = {Kuhl, Christiane K. and Schrading, Simone and Strobel,
                    Kevin and Schild, Hans H. and Hilgers, Ralf-Dieter and
                    Bieling, Heribert B.},
  Title           = {Abbreviated Breast Magnetic Resonance Imaging {(MRI):}
                    {First} Postcontrast Subtracted Images and
                    Maximum-Intensity {Projection—A} Novel Approach to
                    Breast Cancer Screening With {MRI}},
  JournalTitle    = {J. Clin. Oncol.},
  Date            = {2014},
  DOI             = {10.1200/jco.2013.52.5386},
  Keywords        = {Kuhl-Selection},
  Number          = {22},
  Pages           = {2304--2310},
  ShortJournal    = {JCO},
  Subtitle        = {First Postcontrast Subtracted Images and
                    Maximum-Intensity Projection-A Novel Approach to Breast
                    Cancer Screening With MRI},
  Volume          = {32}
}

@Article{Kumar:820092,
  Author          = {Kumar, Neeraj and Hitch, Thomas C. A. and Haller, Dirk
                    and Lagkouvardos, Ilias and Clavel, Thomas},
  Title           = {MiMiC: a bioinformatic approach for generation of
                    synthetic communities from metagenomes},
  JournalTitle    = {Microbial biotechnology},
  Date            = {2021},
  DOI             = {10.1111/1751-7915.13845},
  Keywords        = {Clavel-Selection,CRC1382-Project A05,CRC1382-Project
                    Q02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {1757--1770},
  Volume          = {14}
}

@Article{Kunjachan:196376,
  Author          = {Kunjachan, Sijumon and Gremse, Felix and Theek, Benjamin
                    and Koczera, Patrick and Pola, Robert and Pechar, Michal
                    and Etrych, Tomas and Ulbrich, Karel and Storm, Gert and
                    Kiessling, Fabian and Lammers, Twan},
  Title           = {Noninvasive Optical Imaging of Nanomedicine
                    Biodistribution},
  JournalTitle    = {ACS Nano},
  Date            = {2012},
  DOI             = {10.1021/nn303955n},
  Keywords        = {Gremse-Selection},
  Number          = {1},
  Pages           = {252--262},
  Volume          = {7}
}

@Article{Kunjachan:234425,
  Author          = {Kunjachan, Sijumon and Pola, Robert and Gremse, Felix
                    and Theek, Benjamin and Ehling, Josef and Moeckel, Diana
                    and Hermanns-Sachweh, Benita and Pechar, Michal and
                    Ulbrich, Karel and Hennink, Wim E. and Storm, Gert and
                    Lederle, Wiltrud and Kiessling, Fabian and Lammers,
                    Twan},
  Title           = {Passive versus Active Tumor Targeting Using {RGD}- and
                    {NGR}-Modified Polymeric Nanomedicines},
  JournalTitle    = {Nano Lett.},
  Date            = {2014},
  author+an:default = {13=sharedLast;14=sharedLast},
  DOI             = {10.1021/nl404391r},
  Keywords        = {Kießling-Selection},
  Addendum        = sharedlast,
  Number          = {2},
  Pages           = {972--981},
  Volume          = {14}
}

@Article{Kurt:828359,
  Author          = {Kurt, Berkan and Bündgens, Lukas and Wirtz, Theresa H.
                    and Loosen, Sven H. and Schulze-Hagen, Maximilian and
                    Truhn, Daniel and Brozat, Jonathan F. and Abu Jhaisha,
                    Samira and Hohlstein, Philipp and Koek, Ger and
                    Weiskirchen, Ralf and Trautwein, Christian and Tacke,
                    Frank and Hamesch, Karim and Koch, Alexander},
  Title           = {Serum Perilipin 2 ({PLIN}2) Predicts Multiple Organ
                    Dysfunction in Critically Ill Patients},
  JournalTitle    = {Biomedicines},
  Date            = {2021},
  DOI             = {10.3390/biomedicines9091210},
  Keywords        = {,CRC1382-Project B05,CRC1382-Project A06,CRC1382-Project
                    A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {9},
  Pages           = {1210},
  Volume          = {9}
}

@Article{Labiano2022-ol,
  Author          = {Labiano, Ibone and Agirre-Lizaso, Aloña and Olaizola,
                    Paula and Echebarria, Anne and Huici-Izagirre, Maider and
                    Olaizola, Irene and Esparza-Baquer, Aitor and Sharif,
                    Omar and Hijona, Elizabeth and Milkiewicz, Piotr and
                    Milkiewicz, Malgorzata and González-Romero, Francisco
                    and Aspichueta, Patricia and Monte, Maria J and Marin,
                    Jose J G and Vucur, Mihael and Luedde, Tom and Marzioni,
                    Marco and Mann, Derek A and Bujanda, Luis and Rodrigues,
                    Pedro M and Banales, Jesus M and Perugorria, Maria J},
  Title           = {{TREM-2} plays a protective role in cholestasis by
                    acting as a negative regulator of inflammation},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2022.05.044},
  Keywords        = {TREM receptors; cholangiopathies; inflammation; innate
                    immunity; liver resident macrophages; ursodeoxycholic
                    acid},
  Number          = {4},
  Pages           = {991--1004},
  Volume          = {77}
}

@Article{Lagkouvardos2015,
  Author          = {Lagkouvardos, Ilias and Kläring, Karoline and
                    Heinzmann, Silke S. and Platz, Stefanie and Scholz,
                    Birgit and Engel, Karl-Heinz and Schmitt-Kopplin,
                    Philippe and Haller, Dirk and Rohn, Sascha and Skurk,
                    Thomas and Clavel, Thomas},
  Title           = {Gut metabolites and bacterial community networks during
                    a pilot intervention study with flaxseeds in healthy
                    adult men},
  JournalTitle    = {Mol. Nutr. Food Res.},
  Date            = {2015},
  DOI             = {10.1002/mnfr.201500125},
  Number          = {8},
  Pages           = {1614--1628},
  Volume          = {59}
}

@Article{Lagkouvardos2016,
  Author          = {Lagkouvardos, Ilias and Joseph, Divya and Kapfhammer,
                    Martin and Giritli, Sabahattin and Horn, Matthias and
                    Haller, Dirk and Clavel, Thomas},
  Title           = {{IMNGS:} {A} comprehensive open resource of processed
                    {16S} {rRNA} microbial profiles for ecology and diversity
                    studies},
  JournalTitle    = {Sci. Rep.},
  Date            = {2016},
  DOI             = {10.1038/srep33721},
  Number          = {1},
  Volume          = {6}
}

@Article{Lagkouvardos2019-pd,
  Author          = {Lagkouvardos, Ilias and Lesker, Till R. and Hitch,
                    Thomas C. A. and Gálvez, Eric J. C. and Smit, Nathiana
                    and Neuhaus, Klaus and Wang, Jun and Baines, John F. and
                    Abt, Birte and Stecher, Bärbel and Overmann, Jörg and
                    Strowig, Till and Clavel, Thomas},
  Title           = {Sequence and cultivation study of Muribaculaceae reveals
                    novel species, host preference, and functional potential
                    of this yet undescribed family},
  JournalTitle    = {Microbiome},
  Date            = {2019},
  DOI             = {10.1186/s40168-019-0637-2},
  Number          = {1},
  Pages           = {28},
  Volume          = {7}
}

@Article{Lagkouvardos2016-zz,
  Author          = {Lagkouvardos, Ilias and Pukall, Rüdiger and Abt, Birte
                    and Foesel, Bärbel U. and Meier-Kolthoff, Jan P. and
                    Kumar, Neeraj and Bresciani, Anne and Martínez, Inés
                    and Just, Sarah and Ziegler, Caroline and Brugiroux,
                    Sandrine and Garzetti, Debora and Wenning, Mareike and
                    Bui, Thi P. N. and Wang, Jun and Hugenholtz, Floor and
                    Plugge, Caroline M. and Peterson, Daniel A. and Hornef,
                    Mathias W. and Baines, John F. and Smidt, Hauke and
                    Walter, Jens and Kristiansen, Karsten and Nielsen, Henrik
                    B. and Haller, Dirk and Overmann, Jörg and Stecher,
                    Bärbel and Clavel, Thomas},
  DOI             = {10.1038/nmicrobiol.2016.131},
  Year            = {2016},
  Volume          = {1},
  Keywords        = {Clavel-Selection},
  Number          = {10},
  Title           = {The Mouse Intestinal Bacterial Collection {(miBC)}
                    provides host-specific insight into cultured diversity
                    and functional potential of the gut microbiota},
  JournalTitle    = {Nat. Microbiol.},
}


@Article{Lagkouvardos:683108,
  Author          = {Lagkouvardos, Ilias and Pukall, Rüdiger and Abt, Birte
                    and Foesel, Bärbel U. and Meier-Kolthoff, Jan P. and
                    Kumar, Neeraj and Bresciani, Anne and Martínez, Inés
                    and Just, Sarah and Ziegler, Caroline and Brugiroux,
                    Sandrine and Garzetti, Debora and Wenning, Mareike and
                    Bui, Thi P. N. and Wang, Jun and Hugenholtz, Floor and
                    Plugge, Caroline M. and Peterson, Daniel A. and Hornef,
                    Mathias W. and Baines, John F. and Smidt, Hauke and
                    Walter, Jens and Kristiansen, Karsten and Nielsen, Henrik
                    B. and Haller, Dirk and Overmann, Jörg and Stecher,
                    Bärbel and Clavel, Thomas},
  Title           = {Erratum: {Corrigendum:} The Mouse Intestinal Bacterial
                    Collection {(miBC)} provides host-specific insight into
                    cultured diversity and functional potential of the gut
                    microbiota},
  JournalTitle    = {Nat. Microbiol.},
  Date            = {2016},
  DOI             = {10.1038/nmicrobiol.2016.219},
  Number          = {11},
  Pages           = {16219},
  Volume          = {1}
}

@Article{Lam2018Low-Cost,
  Author          = {Lam, Ka-Lung and Lin, Shaolin and Liu, Chaoran and Wu,
                    Xiyang and Tang, Shuze and Kwan, Hoi-Shan and Cheung,
                    Peter Chi-Keung},
  Title           = {Low-Cost Method Generating \emph{In Situ} Anaerobic
                    Conditions on a 96-Well Plate for Microbial Fermentation
                    in Food Research},
  JournalTitle    = {J. Agr. Food Chem.},
  Date            = {2018-11-07},
  DOI             = {10.1021/acs.jafc.8b04888},
  Number          = {44},
  Pages           = {11839--11845},
  Volume          = {66}
}

@Article{LamasPaz:809360,
  Author          = {Lamas-Paz, Arantza and Morán, Laura and Peng, Jin and
                    Salinas, Beatriz and López-Alcántara, Nuria and Sydor,
                    Svenja and Vilchez-Vargas, Ramiro and Asensio, Iris and
                    Hao, Fengjie and Zheng, Kang and Martín-Adrados, Beatriz
                    and Moreno, Laura and Cogolludo, Angel and Gómez del
                    Moral, Manuel and Bechmann, Lars and Martínez-Naves,
                    Eduardo and Vaquero, Javier and Bañares, Rafael and
                    Nevzorova, Yulia A. and Cubero, Francisco Javier},
  Title           = {Intestinal Epithelial Cell-Derived Extracellular
                    Vesicles Modulate Hepatic Injury via the Gut-Liver Axis
                    During Acute Alcohol Injury},
  JournalTitle    = {Frontiers in pharmacology},
  Date            = {2020},
  DOI             = {10.3389/fphar.2020.603771},
  Keywords        = {,CRC1382-Project A02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {603771},
  Volume          = {11}
}

@Article{Lambrecht:815757,
  Author          = {Lambrecht, Joeri and Tacke, Frank},
  Title           = {Controversies and Opportunities in the Use of
                    Inflammatory Markers for Diagnosis or Risk Prediction in
                    Fatty Liver Disease},
  JournalTitle    = {Front. Immunol.},
  Date            = {2021},
  DOI             = {10.3389/fimmu.2020.634409},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {634409},
  Volume          = {11}
}

@Article{Lambin2012-qe,
  Author          = {Lambin, Philippe and Rios-Velazquez, Emmanuel and
                    Leijenaar, Ralph and Carvalho, Sara and van Stiphout,
                    Ruud G.P.M. and Granton, Patrick and Zegers, Catharina
                    M.L. and Gillies, Robert and Boellard, Ronald and Dekker,
                    André and Aerts, Hugo J.W.L.},
  Title           = {Radiomics: {Extracting} more information from medical
                    images using advanced feature analysis},
  JournalTitle    = {Eur. J. Cancer},
  Date            = {2012},
  DOI             = {10.1016/j.ejca.2011.11.036},
  Number          = {4},
  Pages           = {441--446},
  Volume          = {48}
}

@Article{Lambrecht:828487,
  Author          = {Lambrecht, Joeri and van Grunsven, Leo A. and Tacke,
                    Frank},
  Title           = {Current and emerging pharmacotherapeutic interventions
                    for the treatment of liver fibrosis},
  JournalTitle    = {Expert Opin. Pharmacother.},
  Date            = {2020},
  DOI             = {10.1080/14656566.2020.1774553},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {13},
  Pages           = {1637--1650},
  ShortJournal    = {EOP},
  Volume          = {21}
}

@Article{Lambrecht:828495,
  Author          = {Lambrecht, Joeri and Porsch-Özçürümez, Mustafa and
                    Best, Jan and Jost-Brinkmann, Fabian and Roderburg,
                    Christoph and Demir, Münevver and Tacke, Frank and Mohr,
                    Raphael},
  Title           = {The {APAC} Score},
  JournalTitle    = {J. Clin. Med.},
  Date            = {2021},
  DOI             = {10.3390/jcm10153392},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {15},
  Pages           = {3392},
  Subtitle        = {A Novel and Highly Performant Serological Tool for Early
                    Diagnosis of Hepatocellular Carcinoma in Patients with
                    Liver Cirrhosis},
  Volume          = {10}
}

@Article{Lammers:480705,
  Author          = {Lammers, Twan and Koczera, Patrick and Fokong, Stanley
                    and Gremse, Felix and Ehling, Josef and Vogt, Michael and
                    Pich, Andrij and Storm, Gert and van Zandvoort, Marc and
                    Kiessling, Fabian},
  Title           = {Theranostic {USPIO}-Loaded Microbubbles for Mediating
                    and Monitoring Blood-Brain Barrier Permeation},
  JournalTitle    = {Adv. Funct. Mater.},
  Date            = {2014},
  DOI             = {10.1002/adfm.201401199},
  Keywords        = {Kießling-Selection},
  Number          = {1},
  Pages           = {36--43},
  Volume          = {25}
}

@Article{Lanaspa2012-fr,
  Author          = {Lanaspa, Miguel A and Sanchez-Lozada, Laura G and Choi,
                    Yea-Jin and Cicerchi, Christina and Kanbay, Mehmet and
                    Roncal-Jimenez, Carlos A and Ishimoto, Takuji and Li,
                    Nanxing and Marek, George and Duranay, Murat and
                    Schreiner, George and Rodriguez-Iturbe, Bernardo and
                    Nakagawa, Takahiko and Kang, Duk-Hee and Sautin, Yuri Y
                    and Johnson, Richard J},
  Title           = {Uric acid induces hepatic steatosis by generation of
                    mitochondrial oxidative stress: potential role in
                    fructose-dependent and -independent fatty liver},
  JournalTitle    = {J. Biol. Chem.},
  Date            = {2012},
  DOI             = {10.1074/jbc.M112.399899},
  Number          = {48},
  Pages           = {40732--40744},
  Volume          = {287}
}

@Article{Lau-Corona2020,
  Author          = {Lau-Corona, Dana and Bae, Woo Kyun and Hennighausen,
                    Lothar and Waxman, David J.},
  Title           = {Sex-biased genetic programs in liver metabolism and
                    liver fibrosis are controlled by {EZH1} and {EZH2}},
  JournalTitle    = {PLoS Genet.},
  Date            = {2020},
  DOI             = {10.1371/journal.pgen.1008796},
  Keywords        = {Animals; Disease Models,Animal; Enhancer of Zeste
                    Homolog 2 Protein/*genetics/metabolism; Female; Gene
                    Expression Profiling; Gene Expression Regulation; Gene
                    Knockout Techniques; Histones/metabolism;
                    Liver/*metabolism; Liver Cirrhosis/*genetics/metabolism;
                    Male; Methylation; Mice; Polycomb Repressive Complex
                    2/*genetics/metabolism; Sequence Analysis,RNA; Sex
                    Characteristics},
  Note            = {PMC7263639},
  Number          = {5},
  Pages           = {e1008796},
  Volume          = {16}
}

@Article{Lau2016-sy,
  Author          = {Lau, Eva and Marques, Cláudia and Pestana, Diogo and
                    Santoalha, Mariana and Carvalho, Davide and Freitas,
                    Paula and Calhau, Conceição},
  Title           = {The role of {I-FABP} as a biomarker of intestinal
                    barrier dysfunction driven by gut microbiota changes in
                    obesity},
  JournalTitle    = {Nutr. Metab. (Lond.)},
  Date            = {2016},
  DOI             = {10.1186/s12986-016-0089-7},
  Keywords        = {Gut microbiota; Inflammation; Intestinal fatty acid
                    binding protein; Intestinal permeability; Obesity},
  Number          = {1},
  Pages           = {31},
  Volume          = {13}
}

@Article{Ldde:162330,
  Author          = {Luedde, Tom and Assmus, Ulrike and Wüstefeld, Torsten
                    and Meyer zu Vilsendorf, Andreas and Roskams, Tania and
                    Schmidt-Supprian, Mark and Rajewsky, Klaus and Brenner,
                    David A. and Manns, Michael P. and Pasparakis, Manolis
                    and Trautwein, Christian},
  Title           = {Deletion of {IKK2} in hepatocytes does not sensitize
                    these cells to {TNF}-induced apoptosis but protects from
                    ischemia/reperfusion injury},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2005},
  DOI             = {10.1172/jci23493},
  Keywords        = {Lüdde-Selection},
  Number          = {4},
  Pages           = {849--859},
  Volume          = {115}
}

@Article{Lu2008-gk,
  Author          = {Lu, Mingfang and Varley, Alan W. and Ohta, Shoichiro and
                    Hardwick, John and Munford, Robert S.},
  Title           = {Host Inactivation of Bacterial Lipopolysaccharide
                    Prevents Prolonged Tolerance Following Gram-Negative
                    Bacterial Infection},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2008},
  DOI             = {10.1016/j.chom.2008.06.009},
  Number          = {3},
  Pages           = {293--302},
  Volume          = {4}
}

@Article{Ldde:163595,
  Author          = {Luedde, Tom and Beraza, Naiara and Kotsikoris, Vasileios
                    and van Loo, Geert and Nenci, Arianna and De Vos, Rita
                    and Roskams, Tania and Trautwein, Christian and
                    Pasparakis, Manolis},
  Title           = {Deletion of {NEMO/IKKγ} in Liver Parenchymal Cells
                    Causes Steatohepatitis and Hepatocellular Carcinoma},
  JournalTitle    = {Cancer Cell},
  Date            = {2007},
  DOI             = {10.1016/j.ccr.2006.12.016},
  Keywords        = {Lüdde-Selection},
  Number          = {2},
  Pages           = {119--132},
  Volume          = {11}
}

@Article{Lee2008-zs,
  Author          = {Lee, Seunghee and Lee, Jeongkyung and Lee, Soo-Kyung and
                    Lee, Jae W},
  Title           = {Activating signal cointegrator-2 is an essential adaptor
                    to recruit histone {H3} lysine 4 methyltransferases
                    {MLL3} and {MLL4} to the liver {X} receptors},
  JournalTitle    = {Mol. Endocrinol.},
  Date            = {2008},
  DOI             = {10.1210/me.2008-0012},
  Number          = {6},
  Pages           = {1312--1319},
  Volume          = {22}
}

@Article{Lee2004-au,
  Author          = {Lee, Ju-Seog and Chu, In-Sun and Mikaelyan, Arsen and
                    Calvisi, Diego F and Heo, Jeonghoon and Reddy, Janardan K
                    and Thorgeirsson, Snorri S},
  Title           = {Application of comparative functional genomics to
                    identify best-fit mouse models to study human cancer},
  JournalTitle    = {Nat. Genet.},
  Date            = {2004},
  DOI             = {10.1038/ng1481},
  Number          = {12},
  Pages           = {1306--1311},
  Volume          = {36}
}

@Article{Lee2010-zh,
  Author          = {Lee, Jae Woong and Cho, Yong Kyun and Ryan, Mc and Kim,
                    Hyang and Lee, Seung Won and Chang, Eugene and Joo, Kwan
                    Joong and Kim, Jung Tae and Kim, Bum Soo and Sung, Ki
                    Chul},
  Title           = {Serum uric Acid as a predictor for the development of
                    nonalcoholic Fatty liver disease in apparently healthy
                    subjects: a 5-year retrospective cohort study},
  JournalTitle    = {Gut Liver},
  Date            = {2010},
  DOI             = {10.5009/gnl.2010.4.3.378},
  Keywords        = {Metabolic syndrome; Non-alcoholic fatty liver disease;
                    Uric acid},
  Number          = {3},
  Pages           = {378--383},
  Volume          = {4}
}

@Article{Lee2011,
  Author          = {Lee, Kit Ming and McKimmie, Clive S. and Gilchrist,
                    Derek S. and Pallas, Kenneth J. and Nibbs, Robert J. and
                    Garside, Paul and McDonald, Victoria and Jenkins,
                    Christopher and Ransohoff, Richard and Liu, LiPing and
                    Milling, Simon and Cerovic, Vuk and Graham, Gerard J.},
  Title           = {D6 facilitates cellular migration and fluid flow to
                    lymph nodes by suppressing lymphatic congestion},
  JournalTitle    = {Blood},
  Date            = {2011},
  DOI             = {10.1182/blood-2011-03-344044},
  Keywords        = {Cerovic-Selection},
  Number          = {23},
  Pages           = {6220--6229},
  Volume          = {118}
}

@Article{Lee2019,
  Author          = {Lee, Jae W. and Stone, Meredith L. and Porrett, Paige M.
                    and Thomas, Stacy K. and Komar, Chad A. and Li, Joey H.
                    and Delman, Devora and Graham, Kathleen and Gladney,
                    Whitney L. and Hua, Xia and Black, Taylor A. and Chien,
                    Austin L. and Majmundar, Krishna S. and Thompson, Jeffrey
                    C. and Yee, Stephanie S. and O'Hara, Mark H. and
                    Aggarwal, Charu and Xin, Dong and Shaked, Abraham and
                    Gao, Mingming and Liu, Dexi and Borad, Mitesh J. and
                    Ramanathan, Ramesh K. and Carpenter, Erica L. and Ji,
                    Ailing and de Beer, Maria C. and de Beer, Frederick C.
                    and Webb, Nancy R. and Beatty, Gregory L.},
  Title           = {Hepatocytes direct the formation of a pro-metastatic
                    niche in the liver},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-019-1004-y},
  Number          = {7747},
  Pages           = {249--252},
  Volume          = {567}
}

@Article{Lee:716458,
  Author          = {Lee, Thomas and Clavel, Thomas and Smirnov, Kirill and
                    Schmidt, Annemarie and Lagkouvardos, Ilias and Walker,
                    Alesia and Lucio, Marianna and Michalke, Bernhard and
                    Schmitt-Kopplin, Philippe and Fedorak, Richard and
                    Haller, Dirk},
  Title           = {Oral versus intravenous iron replacement therapy
                    distinctly alters the gut microbiota and metabolome in
                    patients with {IBD}},
  JournalTitle    = {Gut},
  Date            = {2016},
  DOI             = {10.1136/gutjnl-2015-309940},
  Number          = {5},
  Pages           = {863--871},
  Volume          = {66}
}

@Article{Lee2017-ai,
  Author          = {Lee, Thomas and Clavel, Thomas and Smirnov, Kirill and
                    Schmidt, Annemarie and Lagkouvardos, Ilias and Walker,
                    Alesia and Lucio, Marianna and Michalke, Bernhard and
                    Schmitt-Kopplin, Philippe and Fedorak, Richard and
                    Haller, Dirk},
  Title           = {Oral versus intravenous iron replacement therapy
                    distinctly alters the gut microbiota and metabolome in
                    patients with {IBD}},
  JournalTitle    = {Gut},
  Date            = {2016},
  DOI             = {10.1136/gutjnl-2015-309940},
  Keywords        = {ANEMIA; IBD CLINICAL; INFLAMMATORY BOWEL DISEASE;
                    INTESTINAL BACTERIA; IRON DEFICIENCY},
  Number          = {5},
  Pages           = {863--871},
  Volume          = {66}
}

@Article{Metidji2018-pr,
  Author          = {Metidji, Amina and Omenetti, Sara and Crotta, Stefania
                    and Li, Ying and Nye, Emma and Ross, Ellie and Li, Vivian
                    and Maradana, Muralidhara R and Schiering, Chris and
                    Stockinger, Brigitta},
  Title           = {The environmental sensor {AHR} protects from
                    inflammatory damage by maintaining intestinal stem cell
                    homeostasis and barrier integrity},
  JournalTitle    = {Immunity},
  Date            = {2018},
  DOI             = {10.1016/j.immuni.2018.07.010},
  Number          = {2},
  Pages           = {353--362.e5},
  Volume          = {49}
}

@Article{Sorrentino2020-ar,
  Author          = {Sorrentino, Giovanni and Perino, Alessia and Yildiz, Ece
                    and El Alam, Gaby and Bou Sleiman, Maroun and Gioiello,
                    Antimo and Pellicciari, Roberto and Schoonjans,
                    Kristina},
  Title           = {Bile Acids Signal via {TGR5} to Activate Intestinal Stem
                    Cells and Epithelial Regeneration},
  JournalTitle    = {Gastroenterology},
  Date            = {2020},
  DOI             = {10.1053/j.gastro.2020.05.067},
  Keywords        = {GLP1; GPBAR1; HFD; IBD; Secondary Bile Acids},
  Number          = {3},
  Pages           = {956--968.e8},
  Volume          = {159}
}

@Article{Lefere:788068,
  Author          = {Lefere, Sander and Devisscher, Lindsey and Tacke,
                    Frank},
  Title           = {Targeting {CCR}2/5 in the treatment of nonalcoholic
                    steatohepatitis ({NASH}) and fibrosis},
  JournalTitle    = {Expert Opin. Investig. Drugs},
  Date            = {2020},
  DOI             = {10.1080/13543784.2020.1718106},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {89--92},
  Subtitle        = {Opportunities and challenges},
  Volume          = {29}
}

@Article{Lefere:813502,
  Author          = {Lefere, Sander and Püngel, Tobias and Hundertmark, Jana
                    and Penners, Christian and Frank, Anna Katharina and
                    Guillot, Adrien and de Muynck, Kevin and Heymann, Felix
                    and Adarbes, Vanessa and Defrêne, Evelyne and Estivalet,
                    Céline and Geerts, Anja and Devisscher, Lindsey and
                    Wettstein, Guillaume and Tacke, Frank},
  Title           = {Differential effects of selective- and pan-{PPAR}
                    agonists on experimental steatohepatitis and hepatic
                    macrophages},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jhep.2020.04.025},
  Keywords        = {Guillot-Selection,Tacke-Selection,CRC1382-Project
                    B05,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {757--770},
  Volume          = {73}
}

@Article{Lehmann2018-ne,
  Author          = {Lehmann, Jennifer M and Claus, Karina and Jansen,
                    Christian and Pohlmann, Alessandra and Schierwagen,
                    Robert and Meyer, Carsten and Thomas, Daniel and
                    Manekeller, Steffen and Claria, Joan and Strassburg,
                    Christian P and Trautwein, Christian and Wasmuth, Hermann
                    E and Berres, Marie-Luise and Trebicka, Jonel},
  Title           = {Circulating {CXCL10} in cirrhotic portal hypertension
                    might reflect systemic inflammation and predict {ACLF}
                    and mortality},
  JournalTitle    = {Liver Int.},
  Date            = {2018},
  DOI             = {10.1111/liv.13610},
  Keywords        = {ACLF ; chemokines; cirrhosis; portal hypertension;
                    transjugular intrahepatic portosystemic shunt},
  Number          = {5},
  Pages           = {875--884},
  Volume          = {38}
}

@Article{Lehman2007,
  Author          = {Lehman, Constance D. and Gatsonis, Constantine and Kuhl,
                    Christiane K. and Hendrick, R. Edward and Pisano, Etta D.
                    and Hanna, Lucy and Peacock, Sue and Smazal, Stanley F.
                    and Maki, Daniel D. and Julian, Thomas B. and DePeri,
                    Elizabeth R. and Bluemke, David A. and Schnall, Mitchell
                    D.},
  Title           = {{MRI} Evaluation of the Contralateral Breast in Women
                    with Recently Diagnosed Breast Cancer},
  JournalTitle    = {N. Engl. J. Med.},
  Date            = {2007},
  DOI             = {10.1056/nejmoa065447},
  Keywords        = {Kuhl-Selection},
  Number          = {13},
  Pages           = {1295--1303},
  Volume          = {356}
}

@Article{Massafra2016-hs,
  Author          = {Massafra, Vittoria and Ijssennagger, Noortje and
                    Plantinga, Maud and Milona, Alexandra and Ramos Pittol,
                    José M. and Boes, Marianne and van Mil, Saskia W.C.},
  Title           = {Splenic dendritic cell involvement in {FXR}-mediated
                    amelioration of {DSS} colitis},
  JournalTitle    = {Biochimica et Biophysica Acta (BBA) - Molecular Basis of
                    Disease},
  Date            = {2016},
  DOI             = {10.1016/j.bbadis.2015.11.001},
  Keywords        = {Dendritic cells; Farnesoid X receptor; Inflammatory
                    Bowel Disease},
  Number          = {2},
  Pages           = {166--173},
  Volume          = {1862}
}

@Article{Magnuska2022-xp,
  Author          = {Magnuska, Zuzanna Anna and Theek, Benjamin and
                    Darguzyte, Milita and Palmowski, Moritz and Stickeler,
                    Elmar and Schulz, Volkmar and Kießling, Fabian},
  Title           = {Influence of the Computer-Aided Decision Support System
                    Design on Ultrasound-Based Breast Cancer Classification},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2022},
  DOI             = {10.3390/cancers14020277},
  Keywords        = {breast cancer; deep learning; machine learning; medical
                    image analysis; radiomics; ultrasound},
  Number          = {2},
  Pages           = {277},
  Volume          = {14}
}

@Article{Magri2017-ub,
  Author          = {Magri, Giuliana and Comerma, Laura and Pybus, Marc and
                    Sintes, Jordi and Lligé, David and Segura-Garzón,
                    Daniel and Bascones, Sabrina and Yeste, Ada and Grasset,
                    Emilie K. and Gutzeit, Cindy and Uzzan, Mathieu and
                    Ramanujam, Meera and van Zelm, Menno C. and
                    Albero-González, Raquel and Vazquez, Ivonne and
                    Iglesias, Mar and Serrano, Sergi and Márquez, Lucía and
                    Mercade, Elena and Mehandru, Saurabh and Cerutti,
                    Andrea},
  Title           = {Human Secretory {IgM} Emerges from Plasma Cells Clonally
                    Related to Gut Memory B Cells and Targets Highly Diverse
                    Commensals},
  JournalTitle    = {Immunity},
  Date            = {2017},
  DOI             = {10.1016/j.immuni.2017.06.013},
  Keywords        = {IgA; IgM; gut; human; memory B cells; microbiota;
                    mucosa; plasma cells; repertoire},
  Number          = {1},
  Pages           = {118--134.e8},
  Volume          = {47}
}

@Article{Lehnen:699196,
  Author          = {Lehnen, Mathias and Ebert, Birgitta E. and Blank, Lars
                    M.},
  Title           = {A comprehensive evaluation of constraining amino acid
                    biosynthesis in compartmented models for metabolic flux
                    analysis},
  JournalTitle    = {Metab. Eng. Commun.},
  Date            = {2017},
  DOI             = {10.1016/j.meteno.2017.07.001},
  Pages           = {34--44},
  Volume          = {5}
}

@Book{Leifson1960Atlas,
  Author          = {Leifson, Einar},
  Title           = {Atlas of bacterial flagellation},
  Date            = {1960},
  DOI             = {10.5962/bhl.title.7270}
}

@Article{Lenicek:807181,
  Author          = {Lenicek, Martin and Olde Damink, Steven W. M. and
                    Schaap, Frank G.},
  Title           = {Gut Microbes Take It to the Next Level?},
  JournalTitle    = {Hepatology},
  Date            = {2020},
  DOI             = {10.1002/hep.31455},
  Keywords        = {Olde Damink-Selection,CRC1382-Project
                    A07,CRC1382-Project A07},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {1483--1485},
  Subtitle        = {First Insights Into Farnesoid X Receptor Agonists of
                    Microbial Origin},
  Volume          = {72}
}

@Article{Lesker:796359,
  Author          = {Lesker, Till R. and Durairaj, Abilash C. and Gálvez,
                    Eric J. C. and Lagkouvardos, Ilias and Baines, John F.
                    and Clavel, Thomas and Sczyrba, Alexander and McHardy,
                    Alice C. and Strowig, Till},
  Title           = {An Integrated Metagenome Catalog Reveals New Insights
                    into the Murine Gut Microbiome},
  JournalTitle    = {Cell Rep.},
  Date            = {2020},
  DOI             = {10.1016/j.celrep.2020.02.036},
  Keywords        = {,CRC1382-Project A05,CRC1382-Project Q02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {9},
  Pages           = {2909--2922.e6},
  Volume          = {30}
}

@Article{Leuker2001,
  Author          = {Leuker, Christoph E. and Labow, Mark and Müller, Werner
                    and Wagner, Norbert},
  Title           = {Neonatally Induced Inactivation of the Vascular Cell
                    Adhesion Molecule 1 Gene Impairs B Cell Localization and
                    T {Cell–Dependent} Humoral Immune Response},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2001},
  DOI             = {10.1084/jem.193.6.755},
  Keywords        = {Wagner-Selection},
  Number          = {6},
  Pages           = {755--768},
  Volume          = {193}
}

@Article{EASL2009-ax,
  Author          = {{European Association for the Study of the Liver}},
  Title           = {{EASL} Clinical Practice Guidelines: management of
                    cholestatic liver diseases},
  JournalTitle    = {J. Hepatol.},
  Date            = {2009},
  DOI             = {10.1016/j.jhep.2009.04.009},
  Number          = {2},
  Pages           = {237--267},
  Volume          = {51}
}

@InProceedings{Levada:689402,
  Author          = {Levada, Kateryna and Guldiken, Nurdan and Vella, G. and
                    James, L. P. and Haybaeck, J. and Kiemer, A. K. and
                    Kessler, S. M. and Trautwein, Christian and Strnad,
                    Pavel},
  Title           = {{{HSP}72} overexpression protects from liver injury via
                    attenuation of jnk signalling},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/S0168-8278(16)00090-8},
  Organization    = {EASL International Liver Congress, Barcelona (Spain), 13
                    Apr 2016 - 17 Apr 2016},
  Pages           = {PS071},
  Volume          = {64}
}

@Article{Levada:753969,
  Author          = {Levada, Kateryna and Guldiken, Nurdan and Zhang, Xiaoji
                    and Vella, Giovanna and Mo, Fa-Rong and James, Laura P.
                    and Haybaeck, Johannes and Kessler, Sonja M. and Kiemer,
                    Alexandra K. and Ott, Thomas and Hartmann, Daniel and
                    Hüser, Norbert and Ziol, Marianne and Trautwein,
                    Christian and Strnad, Pavel},
  Title           = {Hsp72 protects against liver injury via attenuation of
                    hepatocellular death, oxidative stress, and {JNK}
                    signaling},
  JournalTitle    = {J. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/j.jhep.2018.01.003},
  Keywords        = {Guldiken-Selection,Strnad-Selection},
  Number          = {5},
  Pages           = {996--1005},
  Volume          = {68}
}

@Article{Levy2015-xa,
  Author          = {Levy, Maayan and Thaiss, Christoph A. and Zeevi, David
                    and Dohnalová, Lenka and Zilberman-Schapira, Gili and
                    Mahdi, Jemal Ali and David, Eyal and Savidor, Alon and
                    Korem, Tal and Herzig, Yonatan and Pevsner-Fischer,
                    Meirav and Shapiro, Hagit and Christ, Anette and
                    Harmelin, Alon and Halpern, Zamir and Latz, Eicke and
                    Flavell, Richard A. and Amit, Ido and Segal, Eran and
                    Elinav, Eran},
  Title           = {Microbiota-Modulated Metabolites Shape the Intestinal
                    Microenvironment by Regulating {NLRP6} Inflammasome
                    Signaling},
  JournalTitle    = {Cell},
  Date            = {2015},
  DOI             = {10.1016/j.cell.2015.10.048},
  Number          = {6},
  Pages           = {1428--1443},
  Volume          = {163}
}

@Article{Levy2017-yg,
  Author          = {Levy, Maayan and Kolodziejczyk, Aleksandra A. and
                    Thaiss, Christoph A. and Elinav, Eran},
  Title           = {Dysbiosis and the immune system},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2017},
  DOI             = {10.1038/nri.2017.7},
  Number          = {4},
  Pages           = {219--232},
  Volume          = {17}
}

@Article{Liang2022-gf,
  Author          = {Liang, Yan and Kaneko, Kota and Xin, Bing and Lee, Jin
                    and Sun, Xin and Zhang, Kun and Feng, Gen-Sheng},
  Title           = {Temporal analyses of postnatal liver development and
                    maturation by single-cell transcriptomics},
  JournalTitle    = {Dev. Cell},
  Date            = {2022},
  DOI             = {10.1016/j.devcel.2022.01.004},
  Keywords        = {construction of metabolic zones; endothelial cells;
                    functional maturation of liver; hepatocyte heterogeneity;
                    interaction of macrophages; postnatal liver development;
                    single cell transcriptomics},
  Number          = {3},
  Pages           = {398--414.e5},
  Volume          = {57}
}

@Article{Liebal2022-uj,
  Author          = {Liebal, Ulf W and Ullmann, Lena and Lieven, Christian
                    and Kohl, Philipp and Wibberg, Daniel and Zambanini,
                    Thiemo and Blank, Lars M.},
  Title           = {Ustilago maydis metabolic characterization and growth
                    quantification with a genome-scale metabolic model},
  JournalTitle    = {J. Fungi (Basel)},
  Date            = {2022},
  DOI             = {10.3390/jof8050524},
  Keywords        = {Blank-Selection},
  Number          = {5},
  Pages           = {524},
  Volume          = {8}
}

@Article{Liedtke:191717,
  Author          = {Liedtke, Christian and Bangen, Jörg–Martin and
                    Freimuth, Julia and Beraza, Naiara and Lambertz, Daniela
                    and Cubero, Francisco J. and Hatting, Maximilian and
                    Karlmark, Karlin R. and Streetz, Konrad L. and Krombach,
                    Gabriele A. and Tacke, Frank and Gassler, Nikolaus and
                    Riethmacher, Dieter and Trautwein, Christian},
  Title           = {Loss of Caspase-8 Protects Mice Against
                    Inflammation-Related Hepatocarcinogenesis but Induces
                    Non-Apoptotic Liver Injury},
  JournalTitle    = {Gastroenterology},
  Date            = {2011},
  DOI             = {10.1053/j.gastro.2011.08.037},
  Keywords        = {Hatting-Selection,Liedtke-Selection},
  Number          = {6},
  Pages           = {2176--2187},
  Volume          = {141}
}

@Article{Liepelt2020-ec,
  Author          = {Liepelt, Anke and Hohlstein, Philipp and Gussen, Hendrik
                    and Xue, Jia and Aschenbrenner, Anna C and Ulas, Thomas
                    and Buendgens, Lukas and Warzecha, Klaudia T and
                    Bartneck, Matthias and Luedde, Tom and Trautwein,
                    Christian and Schultze, Joachim L and Koch, Alexander and
                    Tacke, Frank},
  Title           = {Differential gene expression in circulating {CD14+}
                    monocytes indicates the prognosis of critically ill
                    patients with sepsis},
  JournalTitle    = {J. Clin. Med.},
  Date            = {2020},
  DOI             = {10.3390/jcm9010127},
  Keywords        = {ICU; biomarker; innate immunity; monocytes; mortality;
                    prognosis; sepsis},
  Number          = {1},
  Pages           = {127},
  Volume          = {9}
}

@Article{Liepelt:788069,
  Author          = {Liepelt, Anke and Hohlstein, Philipp and Gussen, Hendrik
                    and Xue, Jia and Aschenbrenner, Anna C. and Ulas, Thomas
                    and Bündgens, Lukas and Warzecha, Klaudia Theresa and
                    Bartneck, Matthias and Lüdde, Tom and Trautwein,
                    Christian and Schultze, Joachim L. and Koch, Alexander
                    and Tacke, Frank},
  Title           = {Differential Gene Expression in Circulating {CD}14+
                    Monocytes Indicates the Prognosis of Critically Ill
                    Patients with Sepsis},
  JournalTitle    = {J. Clin. Med.},
  Date            = {2020},
  DOI             = {10.3390/jcm9010127},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project B05,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {127},
  Volume          = {9}
}

@Article{Lindner:481537,
  Author          = {Lindner, Cornelia and Thomsen, Irene and Wahl, Benjamin
                    and Ugur, Milas and Sethi, Maya K and Friedrichsen,
                    Michaela and Smoczek, Anna and Ott, Stephan and Baumann,
                    Ulrich and Suerbaum, Sebastian and Schreiber, Stefan and
                    Bleich, André and Gaboriau-Routhiau, Valérie and
                    Cerf-Bensussan, Nadine and Hazanov, Helena and Mehr,
                    Ramit and Boysen, Preben and Rosenstiel, Philip and
                    Pabst, Oliver},
  Title           = {Diversification of memory B cells drives the continuous
                    adaptation of secretory antibodies to gut microbiota},
  JournalTitle    = {Nat. Immunol.},
  Date            = {2015},
  DOI             = {10.1038/ni.3213},
  ids             = {lidner2015a},
  Keywords        = {Pabst-Selection},
  Number          = {8},
  Pages           = {880--888},
  Volume          = {16}
}

@Article{Vallenet2019-fh,
  Author          = {Vallenet, David and Calteau, Alexandra and Dubois,
                    Mathieu and Amours, Paul and Bazin, Adelme and Beuvin,
                    Mylène and Burlot, Laura and Bussell, Xavier and
                    Fouteau, Stéphanie and Gautreau, Guillaume and Lajus,
                    Aurélie and Langlois, Jordan and Planel, Rémi and
                    Roche, David and Rollin, Johan and Rouy, Zoe and Sabatet,
                    Valentin and Médigue, Claudine},
  Title           = {{MicroScope:} {An} integrated platform for the
                    annotation and exploration of microbial gene functions
                    through genomic, pangenomic and metabolic comparative
                    analysis},
  JournalTitle    = {Nucleic Acids Res.},
  Date            = {2019},
  DOI             = {10.1093/nar/gkz926}
}

@Article{Lindner:789318,
  Author          = {Lindner, Cornelia and Wahl, Benjamin and Föhse, Lisa
                    and Suerbaum, Sebastian and Macpherson, Andrew J. and
                    Prinz, Immo and Pabst, Oliver},
  Title           = {Age, microbiota, and T cells shape diverse individual
                    {IgA} repertoires in the intestine},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2012},
  DOI             = {10.1084/jem.20111980},
  Keywords        = {Pabst-Selection},
  Number          = {2},
  Pages           = {365--377},
  ShortJournal    = {JEM},
  Volume          = {209}
}

@Article{Hov2022-uz,
  Author          = {Hov, Johannes R. and Karlsen, Tom H.},
  Title           = {The microbiota and the gut–liver axis in primary
                    sclerosing cholangitis},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2022},
  DOI             = {10.1038/s41575-022-00690-y}
}

@Article{Liu2016-rl,
  Author          = {Liu, Hui-Xin and Rocha, Clarissa Santos and Dandekar,
                    Satya and Wan, Yu-Jui Yvonne},
  Title           = {Functional analysis of the relationship between
                    intestinal microbiota and the expression of hepatic genes
                    and pathways during the course of liver regeneration},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2015.09.022},
  Keywords        = {Bile acid; Gut-liver axis; Immune response; Metabolism;
                    Partial hepatectomy},
  Number          = {3},
  Pages           = {641--650},
  Volume          = {64}
}

@Article{Atkinson2020-zh,
  Author          = {Atkinson, Stephen R and Grove, Jane I and Liebig,
                    Stephanie and Astbury, Stuart and Vergis, Nikhil and
                    Goldin, Robert and Quaglia, Alberto and Bantel, Heike and
                    Guha, Indra Neil and Thursz, Mark R and Newcombe, Paul
                    and Strnad, Pavel and Aithal, Guruprasad P},
  Title           = {In severe Alcoholic Hepatitis, serum keratin-18
                    fragments are diagnostic, prognostic, and theragnostic
                    biomarkers},
  JournalTitle    = {Am. J. Gastroenterol.},
  Date            = {2020},
  DOI             = {10.14309/ajg.0000000000000912},
  Number          = {11},
  Pages           = {1857--1868},
  Volume          = {115}
}

@Article{Harrison2022-kf,
  Author          = {Harrison, Stephen A and Abdelmalek, Manal F and Neff,
                    Guy and Gunn, Nadege and Guy, Cynthia D and Alkhouri,
                    Naim and Bashir, Mustafa R and Freilich, Bradley and
                    Kohli, Anita and Khazanchi, Arun and Sheikh, Muhammad Y
                    and Leibowitz, Mark and Rinella, Mary E and Siddiqui,
                    Mohammad S and Kipnes, Mark and Moussa, Sam E and Younes,
                    Ziad H and Bansal, Meena and Baum, Seth J and Borg, Brian
                    and Ruane, Peter J and Thuluvath, Paul J and Gottwald,
                    Mildred and Khan, Mujib and Chen, Charles and
                    Melchor-Khan, Liza and Chang, William and DePaoli, Alex M
                    and Ling, Lei and Lieu, Hsiao D},
  Title           = {Aldafermin in patients with non-alcoholic
                    steatohepatitis {(ALPINE} 2/3): {A} randomised,
                    double-blind, placebo-controlled, phase 2b trial},
  JournalTitle    = {The Lancet Gastroenterol. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/s2468-1253(22)00017-6},
  Number          = {7},
  Pages           = {603--616},
  Volume          = {7}
}

@Article{Atkinson2022-aq,
  Author          = {Atkinson, Stephen Rahul and Aly, Mahmoud and Remih,
                    Katharina and Tyson, Luke David and Guldiken, Nurdan and
                    Goldin, Robert and Quaglia, Alberto and Thursz, Mark and
                    Strnad, Pavel},
  Title           = {Serum keratin 19 ({CYFRA21-1}) is a prognostic biomarker
                    in severe alcoholic hepatitis},
  JournalTitle    = {Liver Int.},
  Date            = {2022},
  DOI             = {10.1111/liv.15218},
  Keywords        = {AH; K19; cytokeratin; liver disease; mortality},
  Number          = {5},
  Pages           = {1049--1057},
  Volume          = {42}
}

@Article{Majzoub2021,
  Author          = {Majzoub, Abdul M. and Nayfeh, Tarek and Barnard, Abbey
                    and Munaganuru, Nagambika and Dave, Shravan and Singh,
                    Siddharth and Murad, Mohammad Hassan and Loomba, Rohit},
  Title           = {Systematic review with network meta‐analysis:
                    {Comparative} efficacy of pharmacologic therapies for
                    fibrosis improvement and resolution of {NASH}},
  JournalTitle    = {Aliment. Pharmacol. Ther.},
  Date            = {2021},
  DOI             = {10.1111/apt.16583},
  Number          = {7},
  Pages           = {880--889},
  Volume          = {54}
}

@Article{vanPrehn2021-kl,
  Author          = {van Prehn, Joffrey and Reigadas, Elena and Vogelzang,
                    Erik H. and Bouza, Emilio and Hristea, Adriana and Guery,
                    Benoit and Krutova, Marcela and Norén, Torbjorn and
                    Allerberger, Franz and Coia, John E. and Goorhuis,
                    Abraham and van Rossen, Tessel M. and Ooijevaar, Rogier
                    E. and Burns, Karen and Scharvik Olesen, Bente R. and
                    Tschudin-Sutter, Sarah and Wilcox, Mark H. and
                    Vehreschild, Maria J. G. T. and Fitzpatrick, Fidelma and
                    Kuijper, Ed J.},
  Title           = {{European} Society of Clinical Microbiology and
                    Infectious Diseases: {2021} update on the treatment
                    guidance document for Clostridioides difficile infection
                    in adults},
  JournalTitle    = {Clin. Microbiol. Infec.},
  Date            = {2021},
  DOI             = {10.1016/j.cmi.2021.09.038},
  Pages           = {S1--S21},
  Volume          = {27}
}

@Article{Keller2021-oi,
  Author          = {Keller, Josbert J. and Ooijevaar, Rogier E. and Hvas,
                    Christian L. and Terveer, Elisabeth M. and Lieberknecht,
                    Simone C. and Högenauer, Christoph and Arkkila, Perttu
                    and Sokol, Harry and Gridnyev, Oleksiy and Mégraud,
                    Francis and Kump, Patrizia K. and Nakov, Radislav and
                    Goldenberg, Simon D. and Satokari, Reetta and Tkatch,
                    Sergiy and Sanguinetti, Maurizio and Cammarota, Giovanni
                    and Dorofeev, Andrey and Gubska, Olena and Laniro,
                    Gianluca and Mattila, Eero and Arasaradnam, Ramesh P. and
                    Sarin, Shiv K. and Sood, Ajit and Putignani, Lorenza and
                    Alric, Laurent and Baunwall, Simon M. D. and Kupcinskas,
                    Juozas and Link, Alexander and Goorhuis, Abraham G. and
                    Verspaget, Hein W. and Ponsioen, Cyriel and Hold,
                    Georgina L. and Tilg, Herbert and Kassam, Zain and
                    Kuijper, Ed J. and Gasbarrini, Antonio and Mulder, Chris
                    J. J. and Williams, Horace R. T. and Vehreschild, Maria
                    J. G. T.},
  Title           = {A standardised model for stool banking for faecal
                    microbiota transplantation: {A} consensus report from a
                    multidisciplinary {UEG} working group},
  JournalTitle    = {United European Gastroenterol. J.},
  Date            = {2021},
  DOI             = {10.1177/2050640620967898},
  Number          = {2},
  Pages           = {229--247},
  Volume          = {9}
}

@Article{Cammarota2019-ed,
  Author          = {Cammarota, Giovanni and Ianiro, Gianluca and Kelly,
                    Colleen R and Mullish, Benjamin H and Allegretti, Jessica
                    R and Kassam, Zain and Putignani, Lorenza and Fischer,
                    Monika and Keller, Josbert J and Costello, Samuel Paul
                    and Sokol, Harry and Kump, Patrizia and Satokari, Reetta
                    and Kahn, Stacy A and Kao, Dina and Arkkila, Perttu and
                    Kuijper, Ed J and Vehreschild, Maria J. G. T. and Pintus,
                    Cristina and Lopetuso, Loris and Masucci, Luca and
                    Scaldaferri, Franco and Terveer, E M and Nieuwdorp, Max
                    and López-Sanromán, Antonio and Kupcinskas, Juozas and
                    Hart, Ailsa and Tilg, Herbert and Gasbarrini, Antonio},
  Title           = {International consensus conference on stool banking for
                    faecal microbiota transplantation in clinical practice},
  JournalTitle    = {Gut},
  Date            = {2019},
  DOI             = {10.1136/gutjnl-2019-319548},
  Number          = {12},
  Pages           = {2111--2121},
  Volume          = {68}
}

@Article{Liu2022-cs,
  Author          = {Liu, Dong and Czigany, Zoltan and Heij, Lara R and
                    Bouwense, Stefan A W and van Dam, Ronald and Lang, Sven A
                    and Ulmer, Tom F and Neumann, Ulf P. and Bednarsch, Jan},
  Title           = {The value of platelet-to-lymphocyte ratio as a
                    prognostic marker in cholangiocarcinoma: A systematic
                    review and meta-analysis},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2022},
  DOI             = {10.3390/cancers14020438},
  Number          = {2},
  Pages           = {438},
  Volume          = {14}
}

@Article{Chang2014-zf,
  Author          = {Chang, Pamela V and Hao, Liming and Offermanns, Stefan
                    and Medzhitov, Ruslan},
  Title           = {The microbial metabolite butyrate regulates intestinal
                    macrophage function via histone deacetylase inhibition},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2014},
  DOI             = {10.1073/pnas.1322269111},
  Keywords        = {inflammation; microbiome},
  Number          = {6},
  Pages           = {2247--2252},
  Volume          = {111}
}

@Article{Ianiro2022-pa,
  Author          = {Ianiro, Gianluca and Mullish, Benjamin H and Iqbal,
                    Tariq H and Terveer, Elisabeth M and Baunwall, Simon Mark
                    Dahl and Link, Alexander and Sokol, Harry and Kupcinskas,
                    Juozas and Masucci, Luca and Sanguinetti, Maurizio and
                    Vehreschild, Maria J. G. T. and Hvas, Christian L and
                    Keller, Josbert J and Gasbarrini, Antonio and Kujiper, Ed
                    J and Cammarota, Giovanni},
  Title           = {Minimising the risk of monkeypox virus transmission
                    during faecal microbiota transplantation:
                    {Recommendations} from a {European} expert panel},
  JournalTitle    = {The Lancet Gastroenterol. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/s2468-1253(22)00305-3},
  Number          = {11},
  Pages           = {979--980},
  Volume          = {7}
}

@Article{Liu2016,
  Author          = {Liu, Yang and Cao, Xuetao},
  Title           = {Characteristics and Significance of the Pre-metastatic
                    Niche},
  JournalTitle    = {Cancer Cell},
  Date            = {2016},
  DOI             = {10.1016/j.ccell.2016.09.011},
  Number          = {5},
  Pages           = {668--681},
  Volume          = {30}
}

@Article{Peinado2017,
  Author          = {Peinado, Héctor and Zhang, Haiying and Matei, Irina R.
                    and Costa-Silva, Bruno and Hoshino, Ayuko and Rodrigues,
                    Goncalo and Psaila, Bethan and Kaplan, Rosandra N. and
                    Bromberg, Jacqueline F. and Kang, Yibin and Bissell, Mina
                    J. and Cox, Thomas R. and Giaccia, Amato J. and Erler,
                    Janine T. and Hiratsuka, Sachie and Ghajar, Cyrus M. and
                    Lyden, David},
  Title           = {Pre-metastatic niches: organ-specific homes for
                    metastases},
  JournalTitle    = {Nat. Rev. Cancer},
  Date            = {2017},
  DOI             = {10.1038/nrc.2017.6},
  Number          = {5},
  Pages           = {302--317},
  Volume          = {17}
}

@Article{Liu2022-gl,
  Author          = {Liu, Dong and Heij, Lara R and Czigany, Zoltan and Dahl,
                    Edgar and Dulk, Marcel den and Lang, Sven A and Ulmer,
                    Tom F and Neumann, Ulf P and Bednarsch, Jan},
  Title           = {The prognostic value of neutrophil-to-lymphocyte ratio
                    in cholangiocarcinoma: a systematic review and
                    meta-analysis},
  JournalTitle    = {Sci. Rep.},
  Date            = {2022},
  DOI             = {10.1038/s41598-022-16727-w},
  Number          = {1},
  Pages           = {12691},
  Volume          = {12}
}

@Article{Hagel2016-po,
  Author          = {Hagel, Stefan and Stallmach, Andreas and Vehreschild,
                    Maria},
  Title           = {Fecal Microbiota Transplant in Patients With Re current
                    Clostridium Difficile Infection},
  JournalTitle    = {Deutsches Ärzteblatt international},
  Date            = {2016},
  DOI             = {10.3238/arztebl.2016.0583}
}

@Article{Liu:844276,
  Author          = {Liu, Dong and Heij, Lara Rosaline and Czigany, Zoltan
                    and Dahl, Edgar and Lang, Sven Arke and Ulmer, Tom
                    Florian and Lüdde, Tom and Neumann, Ulf Peter and
                    Bednarsch, Jan},
  Title           = {The role of tumor-infiltrating lymphocytes in
                    cholangiocarcinoma},
  JournalTitle    = {J. Exp. Clin. Cancer Res.},
  Date            = {2022},
  DOI             = {10.1186/s13046-022-02340-2},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project A01,CRC1382-Project
                    A06},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {127},
  Volume          = {41}
}

@Article{Peri2019-io,
  Author          = {Peri, Rosemarie and Aguilar, Rebeca Cruz and Tüffers,
                    Kester and Erhardt, Andreas and Link, Alexander and
                    Ehlermann, Philipp and Angeli, Wolfgang and Frank,
                    Thorsten and Storr, Martin and Glück, Thomas and Sturm,
                    Andreas and Rosien, Ulrich and Tacke, Frank and Bachmann,
                    Oliver and Solbach, Philipp and Stallmach, Andreas and
                    Goeser, Felix and Vehreschild, Maria J. G. T.},
  Title           = {The impact of technical and clinical factors on fecal
                    microbiota transfer outcomes for the treatment of
                    recurrent \textit{Clostridioides difficile} infections in
                    {Germany}},
  JournalTitle    = {United European Gastroenterol. J.},
  Date            = {2019},
  DOI             = {10.1177/2050640619839918},
  Number          = {5},
  Pages           = {716--722},
  Volume          = {7}
}

@Article{Liwinski2020-tt,
  Author          = {Liwinski, Timur and Zenouzi, Roman and John, Clara and
                    Ehlken, Hanno and Rühlemann, Malte C and Bang, Corinna
                    and Groth, Stefan and Lieb, Wolfgang and Kantowski,
                    Marcus and Andersen, Nils and Schachschal, Guido and
                    Karlsen, Tom H and Hov, Johannes R and Rösch, Thomas and
                    Lohse, Ansgar W and Heeren, Joerg and Franke, Andre and
                    Schramm, Christoph},
  Title           = {Alterations of the bile microbiome in primary sclerosing
                    cholangitis},
  JournalTitle    = {Gut},
  Date            = {2019},
  DOI             = {10.1136/gutjnl-2019-318416},
  Keywords        = {anti-bacterial mucosal immunity; bile acid metabolism;
                    biliary endoscopy; enteric bacterial microflora; primary
                    sclerosing cholangitis},
  Number          = {4},
  Pages           = {665--672},
  Volume          = {69}
}

@Article{Lodder2015-wx,
  Author          = {Lodder, Jasper and Denaës, Timothé and Chobert,
                    Marie-Noële and Wan, JingHong and El-Benna, Jamel and
                    Pawlotsky, Jean-Michel and Lotersztajn, Sophie and
                    Teixeira-Clerc, Fatima},
  Title           = {Macrophage autophagy protects against liver fibrosis in
                    mice},
  JournalTitle    = {Autophagy},
  Date            = {2015},
  DOI             = {10.1080/15548627.2015.1058473},
  Number          = {8},
  Pages           = {1280--1292},
  Volume          = {11}
}

@Article{Tacke2015-df,
  Author          = {Tacke, D. and Wisplinghoff, H. and Kretzschmar, A. and
                    Farowski, F. and Koehler, P. and Herweg, J. and Cornely,
                    O.A. and Vehreschild, M. J. G. T.},
  Title           = {First implementation of frozen, capsulized faecal
                    microbiota transplantation for recurrent Clostridium
                    difficile infection into clinical practice in {Europe}},
  JournalTitle    = {Clin. Microbiol. Infec.},
  Date            = {2015},
  DOI             = {10.1016/j.cmi.2015.06.027},
  Number          = {11},
  Pages           = {e82--e84},
  Volume          = {21}
}

@Article{Lodewick:561618,
  Author          = {Lodewick, Toine M. and Roeth, Anjali A.J. and Olde
                    Damink, Steven W.M. and Alizai, Patrick H. and van Dam,
                    Ronald M. and Gassler, Nikolaus and Schneider, Mark and
                    Dello, Simon A.W.G. and Schmeding, Maximilian and Dejong,
                    Cornelis H.C. and Neumann, Ulf P.},
  Title           = {Sarcopenia, obesity and sarcopenic obesity: {Effects} on
                    liver function and volume in patients scheduled for major
                    liver resection},
  JournalTitle    = {J. Cachexia Sarcopenia Muscle},
  Date            = {2015},
  DOI             = {10.1002/jcsm.12018},
  Addendum        = preliminarywork,
  Keywords        = {Neumann-Selection},
  Number          = {2},
  Pages           = {155--163},
  Volume          = {6}
}

@Article{Lodewick:716564,
  Author          = {Lodewick, T.M. and Alizai, P.H. and van Dam, R.M. and
                    Roeth, A.A.J. and Schmeding, M. and Heidenhain, C. and
                    Andert, A. and Gassler, N. and Dejong, C.H.C. and
                    Neumann, U.P.},
  Title           = {Effect of Age on Liver Function in Patients Undergoing
                    Partial Hepatectomy},
  JournalTitle    = {Digest. Surg.},
  Date            = {2017},
  DOI             = {10.1159/000452494},
  ids             = {lodewick2017a},
  Number          = {3},
  Pages           = {233--240},
  Volume          = {34}
}

@Article{Loomba2021-md,
  Author          = {Loomba, Rohit and Friedman, Scott L. and Shulman, Gerald
                    I.},
  Title           = {Mechanisms and disease consequences of nonalcoholic
                    fatty liver disease},
  JournalTitle    = {Cell},
  Date            = {2021},
  DOI             = {10.1016/j.cell.2021.04.015},
  Number          = {10},
  Pages           = {2537--2564},
  Volume          = {184}
}

@Article{Loosen:716735,
  Author          = {Loosen, Sven H. and Roderburg, Christoph and Kauertz,
                    Katja L. and Pombeiro, Inês and Leyh, Catherine and
                    Benz, Fabian and Vucur, Mihael and Longerich, Thomas and
                    Koch, Alexander and Braunschweig, Till and Ulmer, Tom F.
                    and Heidenhain, Christoph and Tacke, Frank and
                    Binnebösel, Marcel and Schmeding, Maximilian and
                    Trautwein, Christian and Neumann, Ulf P. and Luedde,
                    Tom},
  Title           = {Elevated levels of circulating osteopontin are
                    associated with a poor survival after resection of
                    cholangiocarcinoma},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/j.jhep.2017.06.020},
  Keywords        = {Neumann-Selection},
  Number          = {4},
  Pages           = {749--757},
  Volume          = {67}
}

@Article{Loosen:781130,
  Author          = {Loosen, Sven and Schulze-Hagen, Maximilian Franz and
                    Bruners, Philipp and Tacke, Frank and Trautwein,
                    Christian and Kuhl, Christiane K. and Lüdde, Tom and
                    Roderburg, Christoph},
  Title           = {Sarcopenia Is a Negative Prognostic Factor in Patients
                    Undergoing Transarterial Chemoembolization ({TACE}) for
                    Hepatic Malignancies},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2019},
  DOI             = {10.3390/cancers11101503},
  Keywords        = {,CRC1382-Project A04,CRC1382-Project A01,CRC1382-Project
                    B05,CRC1382-Project A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {10},
  Pages           = {1503},
  Volume          = {11}
}

@Article{Lotz2006,
  Author          = {Lotz, Michael and Gütle, Dominique and Walther, Sabrina
                    and Ménard, Sandrine and Bogdan, Christian and Hornef,
                    Mathias W.},
  Title           = {Postnatal acquisition of endotoxin tolerance in
                    intestinal epithelial cells},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2006},
  DOI             = {10.1084/jem.20050625},
  Number          = {4},
  Pages           = {973--984},
  Volume          = {203}
}

@Article{Lucchetti2021-mn,
  Author          = {Lucchetti, Mara and Kaminska, Mathilda and Oluwasegun,
                    Aina Kehinde and Mosig, Alexander S. and Wilmes, Paul},
  Title           = {Emulating the gut–liver axis: {Dissecting} the
                    microbiome's effect on drug metabolism using
                    multiorgan-on-chip models},
  JournalTitle    = {Curr. Opin. Endocr. Metab. Res.},
  Date            = {2021},
  DOI             = {10.1016/j.coemr.2021.03.003},
  Pages           = {94--101},
  Volume          = {18}
}

@Article{Luciani:828414,
  Author          = {Luciani, Cécilia and Hager, Fabian Tobias and Cerovic,
                    Vuk and Lelouard, Hugues},
  Title           = {Dendritic cell functions in the inductive and effector
                    sites of intestinal immunity},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2021},
  DOI             = {10.1038/s41385-021-00448-w},
  Keywords        = {,CRC1382-Project B03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {40--50},
  Volume          = {15}
}

@Article{Luck2015-kg,
  Author          = {Luck, Helen and Tsai, Sue and Chung, Jason and
                    Clemente-Casares, Xavier and Ghazarian, Magar and Revelo,
                    Xavier S and Lei, Helena and Luk, Cynthia T and Shi,
                    Sally Yu and Surendra, Anuradha and Copeland, Julia K and
                    Ahn, Jennifer and Prescott, David and Rasmussen, Brittany
                    A and Chng, Melissa Hui Yen and Engleman, Edgar G and
                    Girardin, Stephen E and Lam, Tony K T and Croitoru,
                    Kenneth and Dunn, Shannon and Philpott, Dana J and
                    Guttman, David S and Woo, Minna and Winer, Shawn and
                    Winer, Daniel A},
  Title           = {Regulation of obesity-related insulin resistance with
                    gut anti-inflammatory agents},
  JournalTitle    = {Cell Metab.},
  Date            = {2015},
  DOI             = {10.1016/j.cmet.2015.03.001},
  Number          = {4},
  Pages           = {527--542},
  Volume          = {21}
}

@Article{Luedde2011-rs,
  Author          = {Luedde, Tom and Schwabe, Robert F},
  Title           = {{NF-$\kappa$B} in the liver--linking injury, fibrosis
                    and hepatocellular carcinoma},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2011},
  DOI             = {10.1038/nrgastro.2010.213},
  Number          = {2},
  Pages           = {108--118},
  Volume          = {8}
}

@Article{Kuscuoglu2021-js,
  Author          = {Kuscuoglu, Deniz and Bewersdorf, Lisa and Wenzel,
                    Kathrin and Gross, Annika and Kobazi Ensari, Gökce and
                    Luo, Yizhao and Kilic, Konrad and Hittatiya, Kanishka and
                    Golob‐Schwarzl, Nicole and Leube, Rudolf E and
                    Preisinger, Christian and George, Jacob and Metwally,
                    Mayada and Eslam, Mohammed and Lampertico, Pietro and
                    Petta, Salvatore and Mangia, Alessandra and Berg, Thomas
                    and Boonstra, Andre and Brouwer, Willem P and Abate,
                    Maria Lorena and Loglio, Alessandro and Sutton, Angela
                    and Nahon, Pierre and Schaefer, Benedikt and Zoller,
                    Heinz and Aigner, Elmar and Trautwein, Christian and
                    Haybaeck, Johannes and Strnad, Pavel},
  Title           = {Dual proteotoxic stress accelerates liver injury via
                    activation of {p62-Nrf2}},
  JournalTitle    = {J. Pathol.},
  Date            = {2021},
  DOI             = {10.1002/path.5643},
  Keywords        = {SERPINA1; aggregate; cirrhosis; inclusion; lipophagy;
                    oxidative stress},
  Number          = {1},
  Pages           = {80--91},
  Volume          = {254}
}

@Article{Lykavieris2008-rj,
  Author          = {Lykavieris, Panayotis and Ducot, Béatrice and Lachaux,
                    Alain and Dabadie, Alain and Broué, Pierre and Sarles,
                    Jacques and Bernard, Olivier and Jacquemin, Emmanuel},
  Title           = {Liver Disease Associated with {ZZ} α1-Antitrypsin
                    Deficiency and Ursodeoxycholic Acid Therapy in Children},
  JournalTitle    = {J. Pediatr. Gastroenterol. Nutr.},
  Date            = {2008},
  DOI             = {10.1097/mpg.0b013e31817b6dfb},
  Number          = {5},
  Pages           = {623--629},
  Volume          = {47}
}

@Article{Mansuy-Aubert2013-ny,
  Author          = {Mansuy-Aubert, Virginie and Zhou, Qiong L. and Xie,
                    Xiangyang and Gong, Zhenwei and Huang, Jun-Yuan and Khan,
                    Abdul R. and Aubert, Gregory and Candelaria, Karla and
                    Thomas, Shantele and Shin, Dong-Ju and Booth, Sarah and
                    Baig, Shahid M. and Bilal, Ahmed and Hwang, Daehee and
                    Zhang, Hui and Lovell-Badge, Robin and Smith, Steven R.
                    and Awan, Fazli R. and Jiang, Zhen Y.},
  Title           = {Imbalance between Neutrophil Elastase and its Inhibitor
                    α1-Antitrypsin in Obesity Alters Insulin Sensitivity,
                    Inflammation, and Energy Expenditure},
  JournalTitle    = {Cell Metab.},
  Date            = {2013},
  DOI             = {10.1016/j.cmet.2013.03.005},
  Number          = {4},
  Pages           = {534--548},
  Volume          = {17}
}

@Article{Lunova:446127,
  Author          = {Lunova, Mariia and Goehring, Claudia and Kuscuoglu,
                    Deniz and Mueller, Katrin and Chen, Yu and Walther, Paul
                    and Deschemin, Jean-Christophe and Vaulont, Sophie and
                    Haybaeck, Johannes and Lackner, Carolin and Trautwein,
                    Christian and Strnad, Pavel},
  Title           = {Hepcidin knockout mice fed with iron-rich diet develop
                    chronic liver injury and liver fibrosis due to lysosomal
                    iron overload},
  JournalTitle    = {J. Hepatol.},
  Date            = {2014},
  DOI             = {10.1016/j.jhep.2014.04.034},
  Keywords        = {Strnad-Selection},
  Number          = {3},
  Pages           = {633--641},
  Volume          = {61}
}

@Article{Luo2018-xj,
  Author          = {Luo, Lina and Aubrecht, Jiri and Li, Dingzhou and
                    Warner, Roscoe L. and Johnson, Kent J. and Kenny, Julia
                    and Colangelo, Jennifer L.},
  Title           = {Assessment of serum bile acid profiles as biomarkers of
                    liver injury and liver disease in humans},
  JournalTitle    = {PLoS One},
  Date            = {2018},
  DOI             = {10.1371/journal.pone.0193824},
  Number          = {3},
  Pages           = {e0193824},
  Volume          = {13}
}

@Article{Luo:716370,
  Author          = {Luo, Chi and Balsa, Eduardo and Thomas, Ajith and
                    Hatting, Maximilian and Jedrychowski, Mark and Gygi,
                    Steven P. and Widlund, Hans R. and Puigserver, Pere},
  Title           = {{ERRα} Maintains Mitochondrial Oxidative Metabolism and
                    Constitutes an Actionable Target in {PGC1α}-Elevated
                    Melanomas},
  JournalTitle    = {Mol. Cancer Res.},
  Date            = {2017},
  DOI             = {10.1158/1541-7786.mcr-17-0143},
  Keywords        = {Hatting-Selection},
  Number          = {10},
  Pages           = {1366--1375},
  Volume          = {15}
}

@Article{Lurje2022,
  Author          = {Lurje, Isabella and Czigany, Zoltan and Eischet, Sarah
                    and Bednarsch, Jan and Ulmer, Tom Florian and Isfort,
                    Peter and Strnad, Pavel and Trautwein, Christian and
                    Tacke, Frank and Neumann, Ulf Peter and Lurje, Georg},
  Title           = {The prognostic impact of preoperative body composition
                    in perihilar and intrahepatic cholangiocarcinoma},
  JournalTitle    = {Hepatology Communications},
  Date            = {2022},
  DOI             = {10.1002/hep4.2004},
  Number          = {9},
  Addendum        = preliminarywork,
  Pages           = {2400--2417},
  Volume          = {6}
}

@Article{Lurje:815761,
  Author          = {Lurje, Isabella and Hammerich, Linda and Tacke, Frank},
  Title           = {Dendritic Cell and T Cell Crosstalk in Liver
                    Fibrogenesis and Hepatocarcinogenesis: Implications for
                    Prevention and Therapy of Liver Cancer},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2020},
  DOI             = {10.3390/ijms21197378},
  Keywords        = {,CRC1382-Project B05,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {19},
  Pages           = {7378},
  Volume          = {21}
}

@Article{Ma2022-dp,
  Author          = {Ma, Jing and Guillot, Adrien and Yang, Zhihong and
                    Mackowiak, Bryan and Hwang, Seonghwan and Park, Ogyi and
                    Peiffer, Brandon J. and Ahmadi, Ali Reza and Melo, Luma
                    and Kusumanchi, Praveen and Huda, Nazmul and Saxena,
                    Romil and He, Yong and Guan, Yukun and Feng, Dechun and
                    Sancho-Bru, Pau and Zang, Mengwei and Cameron, Andrew
                    MacGregor and Bataller, Ramon and Tacke, Frank and Sun,
                    Zhaoli and Liangpunsakul, Suthat and Gao, Bin},
  Title           = {Distinct histopathological phenotypes of severe
                    alcoholic hepatitis suggest different mechanisms driving
                    liver injury and failure},
  JournalTitle    = {J. Clin. Invest.},
  Addendum        = preliminarywork,
  Date            = {2022},
  DOI             = {10.1172/jci157780},
  Number          = {14},
  Volume          = {132}
}

@Article{Mackley2015,
  Author          = {Mackley, Emma C. and Houston, Stephanie and Marriott,
                    Clare L. and Halford, Emily E. and Lucas, Beth and
                    Cerovic, Vuk and Filbey, Kara J. and Maizels, Rick M. and
                    Hepworth, Matthew R. and Sonnenberg, Gregory F. and
                    Milling, Simon and Withers, David R.},
  Title           = {{CCR7}-dependent trafficking of {RORγ+} {ILCs} creates
                    a unique microenvironment within mucosal draining lymph
                    nodes},
  JournalTitle    = {Nat. Commun.},
  Date            = {2015},
  DOI             = {10.1038/ncomms6862},
  Keywords        = {Cerovic-Selection},
  Number          = {1},
  Volume          = {6}
}

@Article{Mai2017,
  Author          = {Mai, Martina and Stengel, Sven and Al-Herwi, Eihab and
                    Peter, Jack and Schmidt, Caroline and Rubio, Ignacio and
                    Stallmach, Andreas and Bruns, Tony},
  Title           = {Genetic variants of {TRAF6} modulate peritoneal immunity
                    and the risk of spontaneous bacterial peritonitis in
                    cirrhosis: {A} combined prospective-retrospective study},
  JournalTitle    = {Sci. Rep.},
  Date            = {2017},
  DOI             = {10.1038/s41598-017-04895-z},
  Number          = {1},
  Volume          = {7}
}

@Article{Malato:197338,
  Author          = {Malato, Yann and Ehedego, Haksier and Al–Masaoudi,
                    Malika and Cubero, Francisco Javier and Bornemann, Jörn
                    and Gassler, Nikolaus and Liedtke, Christian and Beraza,
                    Naiara and Trautwein, Christian},
  Title           = {{NF}-{κB} Essential Modifier Is Required for Hepatocyte
                    Proliferation and the Oval Cell Reaction After Partial
                    Hepatectomy in Mice},
  JournalTitle    = {Gastroenterology},
  Date            = {2012},
  DOI             = {10.1053/j.gastro.2012.08.030},
  Number          = {6},
  Pages           = {1597--1608.e11},
  Volume          = {143}
}

@Article{Malehmir2019-zf,
  Author          = {Malehmir, Mohsen and Pfister, Dominik and Gallage,
                    Suchira and Szydlowska, Marta and Inverso, Donato and
                    Kotsiliti, Elena and Leone, Valentina and Peiseler,
                    Moritz and Surewaard, Bas G. J. and Rath, Dominik and
                    Ali, Adnan and Wolf, Monika Julia and Drescher, Hannah
                    and Healy, Marc E. and Dauch, Daniel and Kroy, Daniela
                    and Krenkel, Oliver and Kohlhepp, Marlene and Engleitner,
                    Thomas and Olkus, Alexander and Sijmonsma, Tjeerd and
                    Volz, Julia and Deppermann, Carsten and Stegner, David
                    and Helbling, Patrick and Nombela-Arrieta, César and
                    Rafiei, Anahita and Hinterleitner, Martina and Rall,
                    Marcel and Baku, Florian and Borst, Oliver and Wilson,
                    Caroline L. and Leslie, Jack and O’Connor, Tracy and
                    Weston, Christopher J. and Chauhan, Abhishek and Adams,
                    David H. and Sheriff, Lozan and Teijeiro, Ana and Prinz,
                    Marco and Bogeska, Ruzhica and Anstee, Natasha and
                    Bongers, Malte N. and Notohamiprodjo, Mike and Geisler,
                    Tobias and Withers, Dominic J. and Ware, Jerry and Mann,
                    Derek A. and Augustin, Hellmut G. and Vegiopoulos,
                    Alexandros and Milsom, Michael D. and Rose, Adam J. and
                    Lalor, Patricia F. and Llovet, Josep M. and Pinyol, Roser
                    and Tacke, Frank and Rad, Roland and Matter, Matthias and
                    Djouder, Nabil and Kubes, Paul and Knolle, Percy A. and
                    Unger, Kristian and Zender, Lars and Nieswandt, Bernhard
                    and Gawaz, Meinrad and Weber, Achim and Heikenwalder,
                    Mathias},
  Title           = {Platelet {GPIbα} is a mediator and potential
                    interventional target for {NASH} and subsequent liver
                    cancer},
  JournalTitle    = {Nat. Med.},
  Date            = {2019},
  DOI             = {10.1038/s41591-019-0379-5},
  Number          = {4},
  Pages           = {641--655},
  Volume          = {25}
}

@Article{Mandato2017-wo,
  Author          = {Mandato, Claudia and Di Nuzzi, Antonella and Vajro,
                    Pietro},
  Title           = {Nutrition and Liver Disease},
  JournalTitle    = {Nutrients},
  Date            = {2017},
  DOI             = {10.3390/nu10010009},
  Number          = {1},
  Pages           = {9},
  Volume          = {10}
}

@Article{Marcos2015,
  Author          = {Marcos, R. and Correia-Gomes, C. and Miranda, H. and
                    Carneiro, F.},
  Title           = {Liver gender dimorphism--insights from quantitative
                    morphology},
  JournalTitle    = {Histol. Histopathol.},
  Date            = {2015},
  DOI             = {10.14670/HH-11-648},
  Keywords        = {Animals; Female; Hepatocytes/ultrastructure; Humans;
                    Kupffer Cells/ultrastructure; Liver/*anatomy {\&}
                    histology/cytology; Male; Sex Characteristics},
  Number          = {12},
  Pages           = {1431--1437},
  Volume          = {30}
}

@Article{Marin2016,
  Author          = {Marin, Veronica and Rosso, Natalia and Dal Ben, Matteo
                    and Raseni, Alan and Boschelle, Manuela and Degrassi,
                    Cristina and Nemeckova, Ivana and Nachtigal, Petr and
                    Avellini, Claudio and Tiribelli, Claudio and Gazzin,
                    Silvia},
  Title           = {An Animal Model for the Juvenile Non-Alcoholic Fatty
                    Liver Disease and Non-Alcoholic Steatohepatitis},
  JournalTitle    = {PLoS One},
  Date            = {2016},
  DOI             = {10.1371/journal.pone.0158817},
  Note            = {PMC4938400},
  Number          = {7},
  Pages           = {e0158817},
  Volume          = {11}
}

@Article{Markle2013,
  Author          = {Markle, Janet G. M. and Frank, Daniel N. and
                    Mortin-Toth, Steven and Robertson, Charles E. and Feazel,
                    Leah M. and Rolle-Kampczyk, Ulrike and von Bergen, Martin
                    and McCoy, Kathy D. and Macpherson, Andrew J. and Danska,
                    Jayne S.},
  Title           = {Sex Differences in the Gut Microbiome Drive
                    Hormone-Dependent Regulation of Autoimmunity},
  JournalTitle    = {Science},
  Date            = {2013},
  DOI             = {10.1126/science.1233521},
  ids             = {markle2013a},
  Keywords        = {von Bergen-Selection},
  Number          = {6123},
  Pages           = {1084--1088},
  Volume          = {339}
}

@Article{Marra:446395,
  Author          = {Marra, Fabio and Tacke, Frank},
  Title           = {Roles for Chemokines in Liver Disease},
  JournalTitle    = {Gastroenterology},
  Date            = {2014},
  DOI             = {10.1053/j.gastro.2014.06.043},
  Number          = {3},
  Pages           = {577--594.e1},
  Volume          = {147}
}

@Article{Matson2021-eh,
  Author          = {Matson, Vyara and Chervin, Carolina Soto and Gajewski,
                    Thomas F.},
  Title           = {Cancer and the {Microbiome—Influence} of the Commensal
                    Microbiota on Cancer, Immune Responses, and
                    Immunotherapy},
  JournalTitle    = {Gastroenterology},
  Date            = {2021},
  DOI             = {10.1053/j.gastro.2020.11.041},
  Number          = {2},
  Pages           = {600--613},
  Volume          = {160}
}

@Article{Mateus2020-xe,
  Author          = {Mateus, André and Kurzawa, Nils and Becher, Isabelle
                    and Sridharan, Sindhuja and Helm, Dominic and Stein,
                    Frank and Typas, Athanasios and Savitski, Mikhail M},
  Title           = {Thermal proteome profiling for interrogating protein
                    interactions},
  JournalTitle    = {Mol. Syst. Biol.},
  Date            = {2020},
  DOI             = {10.15252/msb.20199232},
  Keywords        = {drug discovery; metabolites; protein complexes;
                    proteomics; thermal proteome profiling},
  Number          = {3},
  Pages           = {e9232},
  Volume          = {16}
}

@Article{Mathies2018-df,
  Author          = {Mathies, Franziska and Steffens, Niklas and
                    Kleinschmidt, Doerte and Stuhlmann, Friederike and Huber,
                    Francis J. and Roy, Urmi and Meyer, Thomas and
                    Luetgehetmann, Marc and von Petersdorff, Mareike and
                    Seiz, Oliver and Herkel, Johannes and Schramm, Christoph
                    and Flavell, Richard A. and Gagliani, Nicola and Krebs,
                    Christian and Panzer, Ulf and Abdullah, Zeinab and
                    Strowig, Till and Bedke, Tanja and Huber, Samuel},
  Title           = {Colitis Promotes a Pathological Condition of the Liver
                    in the Absence of Foxp3\textsuperscript{+} Regulatory T
                    Cells},
  JournalTitle    = {J. Immunol.},
  Date            = {2018},
  DOI             = {10.4049/jimmunol.1800711},
  Number          = {12},
  Pages           = {3558--3568},
  Volume          = {201}
}

@Article{Franklin2019-xs,
  Author          = {Franklin, Tyler G. and Pruneda, Jonathan N.},
  Title           = {A High-Throughput Assay for Monitoring Ubiquitination in
                    Real Time},
  JournalTitle    = {Front. Chem.},
  Date            = {2019},
  DOI             = {10.3389/fchem.2019.00816},
  Pages           = {816},
  Volume          = {7}
}

@Article{Schmidt2020-fg,
  Author          = {Schmidt, Marco and Maié, Tiago and Dahl, Edgar and
                    Costa, Ivan G. and Wagner, Wolfgang},
  Title           = {Deconvolution of cellular subsets in human tissue based
                    on targeted {DNA} methylation analysis at individual
                    {CpG} sites},
  JournalTitle    = {BMC Biol.},
  Date            = {2020},
  DOI             = {10.1186/s12915-020-00910-4},
  Number          = {1},
  Pages           = {178},
  Volume          = {18}
}

@Article{Matilla2018effect,
  Author          = {Matilla, Miguel A and Krell, Tino},
  Title           = {The effect of bacterial chemotaxis on host infection and
                    pathogenicity},
  JournalTitle    = {FEMS Microbiol. Rev.},
  Date            = {2018-01-01},
  DOI             = {10.1093/femsre/fux052},
  Note            = {[Online; accessed 2019-06-04]},
  Number          = {1},
  Volume          = {42}
}

@Article{Mattos2020Spontaneous,
  Author          = {Mattos, Angelo A. and Wiltgen, Denusa and Jotz, Raquel
                    F. and Dornelles, Caroline M.R. and Fernandes, Matheus V.
                    and Mattos, Ângelo Z.},
  Title           = {Spontaneous bacterial peritonitis and extraperitoneal
                    infections in patients with cirrhosis},
  JournalTitle    = {Ann. Hepatol.},
  Date            = {2020-09},
  DOI             = {10.1016/j.aohep.2020.04.010},
  Number          = {5},
  Pages           = {451--457},
  Volume          = {19}
}

@Article{McKay2000-dw,
  Author          = {McKay, T R and MacVinish, L J and Carpenter, B and
                    Themis, M and Jezzard, S and Goldin, R and Pavirani, A
                    and Hickman, M E and Cuthbert, A W and Coutelle, C},
  Title           = {Selective in vivo transfection of murine biliary
                    epithelia using polycation-enhanced adenovirus},
  JournalTitle    = {Gene Ther.},
  Date            = {2000},
  DOI             = {10.1038/sj.gt.3301144},
  Number          = {8},
  Pages           = {644--652},
  Volume          = {7}
}

@Article{Menard2008,
  Author          = {Ménard, Sandrine and Förster, Valentina and Lotz,
                    Michael and Gütle, Dominique and Duerr, Claudia U. and
                    Gallo, Richard L. and Henriques-Normark, Birgitta and
                    Pütsep, Katrin and Andersson, Mats and Glocker, Erik O.
                    and Hornef, Mathias W.},
  Title           = {Developmental switch of intestinal antimicrobial peptide
                    expression},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2008},
  DOI             = {10.1084/jem.20071022},
  Number          = {1},
  Pages           = {183--193},
  Volume          = {205}
}

@Article{Martini2017-xm,
  Author          = {Martini, Eva and Krug, Susanne M. and Siegmund, Britta
                    and Neurath, Markus F. and Becker, Christoph},
  Title           = {Mend your fences: The epithelial barrier and its
                    relationship with mucosal immunity in inflammatory bowel
                    disease},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/j.jcmgh.2017.03.007},
  Number          = {1},
  Pages           = {33--46},
  Volume          = {4}
}

@Article{Molmenti1993-cj,
  Author          = {Molmenti, E P and Perlmutter, D H and Rubin, D C},
  Title           = {Cell-specific expression of alpha 1-antitrypsin in human
                    intestinal epithelium.},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {1993},
  DOI             = {10.1172/jci116797},
  Number          = {4},
  Pages           = {2022--2034},
  Volume          = {92}
}

@Article{Merad2013-yi,
  Author          = {Merad, Miriam and Sathe, Priyanka and Helft, Julie and
                    Miller, Jennifer and Mortha, Arthur},
  Title           = {The Dendritic Cell Lineage: {Ontogeny} and Function of
                    Dendritic Cells and Their Subsets in the Steady State and
                    the Inflamed Setting},
  JournalTitle    = {Annu. Rev. Immunol.},
  Date            = {2013},
  DOI             = {10.1146/annurev-immunol-020711-074950},
  Number          = {1},
  Pages           = {563--604},
  Volume          = {31}
}

@Article{Meriin2010-sz,
  Author          = {Meriin, Anatoli B. and Wang, Yan and Sherman, Michael
                    Y.},
  Title           = {Isolation of Aggresomes and Other Large Aggregates},
  JournalTitle    = {Curr. Prot. Cell Biology},
  Date            = {2010},
  DOI             = {10.1002/0471143030.cb0338s48},
  Number          = {1},
  Pages           = {Unit 3.38.1--9},
  Volume          = {48}
}

@Article{Mencin2007-jk,
  Author          = {Mencin, Ali and Seki, Ekihiro and Osawa, Yosuke and
                    Kodama, Yuzo and De Minicis, Samuele and Knowles, Michael
                    and Brenner, David A.},
  Title           = {Alpha-1 antitrypsin Z protein {(PiZ)} increases hepatic
                    fibrosis in a murine model of cholestasis},
  JournalTitle    = {Hepatology},
  Date            = {2007},
  DOI             = {10.1002/hep.21832},
  Number          = {5},
  Pages           = {1443--1452},
  Volume          = {46}
}

@Article{Mendler:791935,
  Author          = {Mendler, A. and Pierzchalski, A. and Bauer, M. and
                    Röder, S. and Sattler, A. and Standl, M. and Borte, M.
                    and von Bergen, Martin and Rolle-Kampczyk, U. and
                    Herberth, G.},
  Title           = {{MAIT} cell activation in adolescents is impacted by
                    bile acid concentrations and body weight},
  JournalTitle    = {Clin. Exp. Immunol.},
  Date            = {2020},
  DOI             = {10.1111/cei.13423},
  Keywords        = {,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {199--213},
  Volume          = {200}
}

@Article{Mengers2022-xw,
  Author          = {Mengers, Hendrik G and Westarp, William Graf von and
                    Brücker, Daniela and Jupke, Andreas and Blank, Lars M},
  Title           = {Yeast-based production and in situ purification of
                    acetaldehyde},
  JournalTitle    = {Bioprocess Biosyst. Eng.},
  Date            = {2022},
  DOI             = {10.1007/s00449-022-02697-w},
  Keywords        = {Blank-Selection},
  Number          = {4},
  Pages           = {761--769},
  Volume          = {45}
}

@Article{Meyer2021-ts,
  Author          = {Meyer, Fernando and Lesker, Till-Robin and Koslicki,
                    David and Fritz, Adrian and Gurevich, Alexey and Darling,
                    Aaron E and Sczyrba, Alexander and Bremges, Andreas and
                    McHardy, Alice C},
  Title           = {Tutorial: assessing metagenomics software with the
                    {CAMI} benchmarking toolkit},
  JournalTitle    = {Nat. Protoc.},
  Date            = {2021},
  DOI             = {10.1038/s41596-020-00480-3},
  Number          = {4},
  Pages           = {1785--1801},
  Volume          = {16}
}

@Article{Michalopoulos2021-gn,
  Author          = {Michalopoulos, George K},
  Title           = {Novel insights into liver homeostasis and regeneration},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1038/s41575-021-00454-0},
  Number          = {6},
  Pages           = {369--370},
  Volume          = {18}
}

@Article{Michalopoulos2021-nx,
  Author          = {Michalopoulos, George K. and Bhushan, Bharat},
  Title           = {Liver regeneration: {Biological} and pathological
                    mechanisms and implications},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2020},
  DOI             = {10.1038/s41575-020-0342-4},
  Number          = {1},
  Pages           = {40--55},
  Volume          = {18}
}

@Article{Mikami2014-cd,
  Author          = {Mikami, Yohei and Mizuno, Shinta and Nakamoto, Nobuhiro
                    and Hayashi, Atsushi and Sujino, Tomohisa and Sato,
                    Toshiro and Kamada, Nobuhiko and Matsuoka, Katsuyoshi and
                    Hisamatsu, Tadakazu and Ebinuma, Hirotoshi and Hibi,
                    Toshifumi and Yoshimura, Akihiko and Kanai, Takanori},
  Title           = {Macrophages and dendritic cells emerge in the liver
                    during intestinal inflammation and predispose the liver
                    to inflammation},
  JournalTitle    = {PLoS One},
  Date            = {2014},
  DOI             = {10.1371/journal.pone.0084619},
  Number          = {1},
  Pages           = {e84619},
  Volume          = {9}
}

@Article{Mirchandani2014,
  Author          = {Mirchandani, Ananda S. and Besnard, Anne-Gaelle and Yip,
                    Edwin and Scott, Charlotte and Bain, Calum C. and
                    Cerovic, Vuk and Salmond, Robert J. and Liew, Foo Y.},
  Title           = {Type 2 Innate Lymphoid Cells Drive {CD4+} Th2 Cell
                    Responses},
  JournalTitle    = {J. Immunol.},
  Date            = {2014},
  DOI             = {10.4049/jimmunol.1300974},
  Keywords        = {Cerovic-Selection},
  Number          = {5},
  Pages           = {2442--2448},
  Volume          = {192}
}

@Article{Bjursell2013-uc,
  Author          = {Bjursell, Mikael and Wedin, Marianne and Admyre,
                    Therése and Hermansson, Majlis and Böttcher, Gerhard
                    and Göransson, Melker and Lindén, Daniel and Bamberg,
                    Krister and Oscarsson, Jan and Bohlooly-Y, Mohammad},
  Title           = {Ageing Fxr Deficient Mice Develop Increased Energy
                    Expenditure, Improved Glucose Control and Liver Damage
                    Resembling {NASH}},
  JournalTitle    = {PLoS ONE},
  Date            = {2013},
  DOI             = {10.1371/journal.pone.0064721},
  Number          = {5},
  Pages           = {e64721},
  Volume          = {8}
}

@Article{Misselwitz:807345,
  Author          = {Misselwitz, Benjamin and Wyss, Annika and Raselli, Tina
                    and Cerovic, Vuk and Sailer, Andreas W. and Krupka,
                    Niklas and Ruiz, Florian and Pot, Caroline and Pabst,
                    Oliver},
  Title           = {The oxysterol receptor {GPR}183 in inflammatory bowel
                    diseases},
  JournalTitle    = {Br. J. Pharmacol.},
  Date            = {2021},
  DOI             = {10.1111/bph.15311},
  Keywords        = {,CRC1382-Project B03,CRC1382-Project B06,CRC1382-Project
                    Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {16},
  Pages           = {3140--3156},
  Volume          = {178}
}

@Article{Modest2018-nh,
  Author          = {Modest, D P and Denecke, T and Pratschke, J and Ricard,
                    I and Lang, H and Bemelmans, M and Becker, T and Rentsch,
                    M and Seehofer, D and Bruns, C J and Gebauer, B and
                    Modest, H I and Held, S and Folprecht, G and Heinemann, V
                    and Neumann, U P},
  Title           = {Surgical treatment options following chemotherapy plus
                    cetuximab or bevacizumab in metastatic colorectal
                    cancer-central evaluation of {FIRE-3}},
  JournalTitle    = {Eur. J. Cancer},
  Addendum        = preliminarywork,
  Date            = {2018},
  DOI             = {10.1016/j.ejca.2017.10.028},
  Keywords        = {Neumann-Selection},
  Pages           = {77--86},
  Volume          = {88}
}

@Article{Monteiro:815754,
  Author          = {Monteiro, Sofia and Grandt, Josephine and Uschner, Frank
                    Erhard and Kimer, Nina and Madsen, Jan Lysgård and
                    Schierwagen, Robert and Klein, Sabine and Welsch,
                    Christoph and Schäfer, Liliana and Jansen, Christian and
                    Claria, Joan and Alcaraz-Quiles, José and Arroyo,
                    Vicente and Moreau, Richard and Fernandez, Javier and
                    Bendtsen, Flemming and Mehta, Gautam and Gluud, Lise
                    Lotte and Møller, Søren and Praktiknjo, Michael and
                    Trebicka, Jonel},
  Title           = {Differential inflammasome activation predisposes to
                    acute-on-chronic liver failure in human and experimental
                    cirrhosis with and without previous decompensation},
  JournalTitle    = {Gut},
  Date            = {2021},
  DOI             = {10.1136/gutjnl-2019-320170},
  ids             = {monteiro_differential_2021},
  Keywords        = {Trebicka-Selection,CRC1382-Project A09,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {379--387},
  Volume          = {70}
}

@Article{Moreau2020-si,
  Author          = {Moreau, Richard and Clària, Joan and Aguilar, Ferran
                    and Fenaille, François and Lozano, Juan José and Junot,
                    Christophe and Colsch, Benoit and Caraceni, Paolo and
                    Trebicka, Jonel and Pavesi, Marco and Alessandria, Carlo
                    and Nevens, Frederik and Saliba, Faouzi and Welzel, Tania
                    M and Albillos, Agustin and Gustot, Thierry and
                    Fernández, Javier and Moreno, Christophe and
                    Baldassarre, Maurizio and Zaccherini, Giacomo and Piano,
                    Salvatore and Montagnese, Sara and Vargas, Victor and
                    Genescà, Joan and Solà, Elsa and Bernal, William and
                    Butin, Noémie and Hautbergue, Thaı̈s and Cholet,
                    Sophie and Castelli, Florence and Jansen, Christian and
                    Steib, Christian and Campion, Daniela and Mookerjee, Raj
                    and Rodrı́guez-Gandı́a, Miguel and Soriano, German
                    and Durand, François and Benten, Daniel and Bañares,
                    Rafael and Stauber, Rudolf E and Gronbaek, Henning and
                    Coenraad, Minneke J and Ginès, Pere and Gerbes,
                    Alexander and Jalan, Rajiv and Bernardi, Mauro and
                    Arroyo, Vicente and Angeli, Paolo and {CANONIC Study
                    Investigators of the EASL Clif Consortium} and {Grifols
                    Chair} and {European Foundation for the Study of Chronic
                    Liver Failure (EF Clif)}},
  Title           = {Blood metabolomics uncovers inflammation-associated
                    mitochondrial dysfunction as a potential mechanism
                    underlying {ACLF}},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jhep.2019.11.009},
  ids             = {moreau_blood_2020},
  Number          = {4},
  Pages           = {688--701},
  Volume          = {72}
}

@Article{Mossanen2019-le,
  Author          = {Mossanen, Jana C and Kohlhepp, Marlene and Wehr,
                    Alexander and Krenkel, Oliver and Liepelt, Anke and
                    Roeth, Anjali A and Möckel, Diana and Heymann, Felix and
                    Lammers, Twan and Gassler, Nikolaus and Hermann, Juliane
                    and Jankowski, Joachim and Neumann, Ulf P and Luedde, Tom
                    and Trautwein, Christian and Tacke, Frank},
  Title           = {{CXCR6} inhibits hepatocarcinogenesis by promoting
                    natural killer {T-} and {CD4+} T-cell-dependent control
                    of senescence},
  JournalTitle    = {Gastroenterology},
  Date            = {2019},
  DOI             = {10.1053/j.gastro.2019.01.247},
  Keywords        = {Tacke-Selection},
  Number          = {6},
  Pages           = {1877--1889.e4},
  Volume          = {156}
}

@Article{Mossanen:684997,
  Author          = {Mossanen, Jana C. and Krenkel, Oliver and Ergen, Can and
                    Govaere, Olivier and Liepelt, Anke and Puengel, Tobias
                    and Heymann, Felix and Kalthoff, Sandra and Lefebvre,
                    Eric and Eulberg, Dirk and Luedde, Tom and Marx, Gernot
                    and Strassburg, Christian P. and Roskams, Tania and
                    Trautwein, Christian and Tacke, Frank},
  Title           = {Chemokine {(C}-C motif) receptor 2-positive monocytes
                    aggravate the early phase of acetaminophen-induced acute
                    liver injury},
  JournalTitle    = {Hepatology},
  Date            = {2016},
  DOI             = {10.1002/hep.28682},
  Number          = {5},
  Pages           = {1667--1682},
  Subtitle        = {Mossanen, Krenkel, et al.},
  Volume          = {64}
}

@Article{Mossanen:788070,
  Author          = {Mossanen, Jana C. and Jansen, Tobias U. and Pracht,
                    Jessica and Liepelt, Anke and Bündgens, Lukas and
                    Stoppe, Christian and Goetzenich, Andreas and Simon,
                    Tim-Philipp and Autschbach, Rüdiger and Marx, Gernot and
                    Tacke, Frank},
  Title           = {Elevated circulating {CD}14++{CD}16+ intermediate
                    monocytes are independently associated with extracardiac
                    complications after cardiac surgery},
  JournalTitle    = {Sci. Rep.},
  Date            = {2020},
  DOI             = {10.1038/s41598-020-57700-9},
  ids             = {mossanen2016a},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {947},
  Volume          = {10}
}

@Article{Movahedi2008-yx,
  Author          = {Movahedi, Kiavash and Guilliams, Martin and Van den
                    Bossche, Jan and Van den Bergh, Rafael and Gysemans,
                    Conny and Beschin, Alain and De Baetselier, Patrick and
                    Van Ginderachter, Jo A},
  Title           = {Identification of discrete tumor-induced myeloid-derived
                    suppressor cell subpopulations with distinct {T}
                    cell-suppressive activity},
  JournalTitle    = {Blood},
  Date            = {2008},
  DOI             = {10.1182/blood-2007-07-099226},
  Number          = {8},
  Pages           = {4233--4244},
  Volume          = {111}
}

@Article{Muller2014,
  Author          = {Muller, Paul Andrew and Koscsó, Balázs and Rajani,
                    Gaurav Manohar and Stevanovic, Korey and Berres,
                    Marie-Luise and Hashimoto, Daigo and Mortha, Arthur and
                    Leboeuf, Marylene and Li, Xiu-Min and Mucida, Daniel and
                    Stanley, E. Richard and Dahan, Stephanie and Margolis,
                    Kara Gross and Gershon, Michael David and Merad, Miriam
                    and Bogunovic, Milena},
  Title           = {Crosstalk between Muscularis Macrophages and Enteric
                    Neurons Regulates Gastrointestinal Motility},
  JournalTitle    = {Cell},
  Date            = {2014},
  DOI             = {10.1016/j.cell.2014.04.050},
  Number          = {2},
  Pages           = {300--313},
  Volume          = {158}
}

@Article{Murthy:838779,
  Author          = {Murthy, Supriya and Karkossa, Isabel and Schmidt,
                    Caroline and Hoffmann, Anne and Hagemann, Tobias and
                    Rothe, Kathrin and Seifert, Olga and Anderegg, Ulf and
                    von Bergen, Martin and Schubert, Kristin and Rossol,
                    Manuela},
  Title           = {Danger signal extracellular calcium initiates
                    differentiation of monocytes into
                    {SPP}1/osteopontin-producing macrophages},
  JournalTitle    = {Cell Death Dis.},
  Date            = {2022},
  DOI             = {10.1038/s41419-022-04507-3},
  Keywords        = {CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {53},
  Volume          = {13}
}

@Article{Song2020-du,
  Author          = {Song, Xinyang and Sun, Ximei and Oh, Sungwhan F and Wu,
                    Meng and Zhang, Yanbo and Zheng, Wen and Geva-Zatorsky,
                    Naama and Jupp, Ray and Mathis, Diane and Benoist,
                    Christophe and Kasper, Dennis L},
  Title           = {Microbial bile acid metabolites modulate gut
                    {ROR$\gamma$+} regulatory {T} cell homeostasis},
  JournalTitle    = {Nature},
  Date            = {2020},
  DOI             = {10.1038/s41586-019-1865-0},
  Number          = {7790},
  Pages           = {410--415},
  Volume          = {577}
}

@Article{Muschaweck:834552,
  Author          = {Muschaweck, Moritz and Kopplin, Lydia and Ticconi, Fabio
                    and Schippers, Angela and Iljazovic, Aida and Gálvez,
                    Eric J. C. and Abdallah, Ali T. and Wagner, Norbert and
                    Costa, Ivan G. and Strowig, Till and Pabst, Oliver},
  Title           = {Cognate recognition of microbial antigens defines
                    constricted {CD}4$^{+}$ T cell receptor repertoires in
                    the inflamed colon},
  JournalTitle    = {Immunity},
  Date            = {2021},
  DOI             = {10.1016/j.immuni.2021.08.014},
  Keywords        = {Wagner-Selection,Schippers-Selection,Pabst-Selection,CRC1382-Project
                    B06,CRC1382-Project Q04,CRC1382-Project
                    B02,CRC1382-Project B02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {11},
  Pages           = {2565--2577.e6},
  Volume          = {54}
}

@Article{Nakagaki2018-fc,
  Author          = {Nakagaki, Brenda Naemi and Mafra, Kassiana and de
                    Carvalho, Érika and Lopes, Mateus Eustáquio and
                    Carvalho-Gontijo, Raquel and de Castro-Oliveira,
                    Hortência Maciel and Campolina-Silva, Gabriel Henrique
                    and de Miranda, Camila Dutra Moreira and Antunes, Maísa
                    Mota and Silva, Ana Carolina Carvalho and Diniz, Ariane
                    Barros and Alvarenga, Débora Moreira and Lopes, Maria
                    Alice Freitas and de Souza Lacerda, Viviane Aparecida and
                    Mattos, Matheus Silvério and Araújo, Alan Moreira and
                    Vidigal, Paula Vieira Teixeira and Lima, Cristiano Xavier
                    and Mahecha, Germán A.B. and Madeira, Mila Fernandes
                    Moreira and Fernandes, Gabriel Rocha and Nogueira, Raquel
                    Ferraz and Moreira, Thais Garcias and David, Bruna
                    Araújo and Rezende, Rafael Machado and Menezes, Gustavo
                    Batista},
  Title           = {Immune and metabolic shifts during neonatal development
                    reprogram liver identity and function},
  JournalTitle    = {J. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/j.jhep.2018.08.018},
  Keywords        = {Diet; Early weaning; Immune system; Immunity; In vivo
                    imaging; Metabolism; Newborn},
  Number          = {6},
  Pages           = {1294--1307},
  Volume          = {69}
}

@Article{Mouries2019-ty,
  Author          = {Mouries, Juliette and Brescia, Paola and Silvestri,
                    Alessandra and Spadoni, Ilaria and Sorribas, Marcel and
                    Wiest, Reiner and Mileti, Erika and Galbiati, Marianna
                    and Invernizzi, Pietro and Adorini, Luciano and Penna,
                    Giuseppe and Rescigno, Maria},
  Title           = {Microbiota-driven gut vascular barrier disruption is a
                    prerequisite for non-alcoholic steatohepatitis
                    development},
  JournalTitle    = {J. Hepatol.},
  Date            = {2019},
  DOI             = {10.1016/j.jhep.2019.08.005},
  Number          = {6},
  Pages           = {1216--1228},
  Volume          = {71}
}

@Article{Han2022-ci,
  Author          = {Han, Geongoo and Luong, Hien and Vaishnava, Shipra},
  Title           = {Low abundance members of the gut microbiome exhibit high
                    immunogenicity},
  JournalTitle    = {Gut Microbes},
  Date            = {2022},
  DOI             = {10.1080/19490976.2022.2104086},
  Number          = {1},
  Pages           = {2104086},
  Volume          = {14}
}

@Article{Bonnardel2019-nm,
  Author          = {Bonnardel, Johnny and T'Jonck, Wouter and Gaublomme,
                    Djoere and Browaeys, Robin and Scott, Charlotte L and
                    Martens, Liesbet and Vanneste, Bavo and De Prijck, Sofie
                    and Nedospasov, Sergei A and Kremer, Anna and Van Hamme,
                    Evelien and Borghgraef, Peter and Toussaint, Wendy and De
                    Bleser, Pieter and Mannaerts, Inge and Beschin, Alain and
                    van Grunsven, Leo A and Lambrecht, Bart N and Taghon, Tom
                    and Lippens, Saskia and Elewaut, Dirk and Saeys, Yvan and
                    Guilliams, Martin},
  Title           = {Stellate cells, hepatocytes, and endothelial cells
                    imprint the Kupffer cell identity on monocytes colonizing
                    the liver macrophage niche},
  JournalTitle    = {Immunity},
  Date            = {2019},
  DOI             = {10.1016/j.immuni.2019.08.017},
  Number          = {4},
  Pages           = {638--654.e9},
  Volume          = {51}
}

@Article{De_Simone2021-le,
  Author          = {De Simone, Giorgia and Andreata, Francesco and Bleriot,
                    Camille and Fumagalli, Valeria and Laura, Chiara and
                    Garcia-Manteiga, José M. and Di Lucia, Pietro and
                    Gilotto, Stefano and Ficht, Xenia and De Ponti, Federico
                    F. and Bono, Elisa B. and Giustini, Leonardo and Ambrosi,
                    Gioia and Mainetti, Marta and Zordan, Paola and
                    Bénéchet, Alexandre P. and Ravà, Micol and Chakarov,
                    Svetoslav and Moalli, Federica and Bajenoff, Marc and
                    Guidotti, Luca G. and Ginhoux, Florent and Iannacone,
                    Matteo},
  Title           = {Identification of a Kupffer cell subset capable of
                    reverting the T cell dysfunction induced by
                    hepatocellular priming},
  JournalTitle    = {Immunity},
  Date            = {2021},
  DOI             = {10.1016/j.immuni.2021.05.005},
  Keywords        = {CD8(+) T cells; Kupffer cells; T cell dysfunction;
                    hepatitis B virus; imaging; interleukin-2; liver;
                    scRNA-seq; single cell; tolerance},
  Number          = {9},
  Pages           = {2089--2100.e8},
  Volume          = {54}
}

@Article{Navis2019-xa,
  Author          = {Navis, Marit and Martins Garcia, Tânia and Renes,
                    Ingrid B and Vermeulen, Jacqueline LM and Meisner, Sander
                    and Wildenberg, Manon E and van den Brink, Gijs R and van
                    Elburg, Ruurd M and Muncan, Vanesa},
  Title           = {Mouse fetal intestinal organoids: {New} model to study
                    epithelial maturation from suckling to weaning},
  JournalTitle    = {EMBO Rep.},
  Date            = {2018},
  DOI             = {10.15252/embr.201846221},
  Keywords        = {brush border enzymes; intrinsic intestinal epithelial
                    maturation; mouse fetal organoids; suckling-to-weaning
                    transition},
  Number          = {2},
  Pages           = {e46221},
  Volume          = {20}
}

@Article{NazariJahantigh:196322,
  Author          = {Nazari-Jahantigh, Maliheh and Wei, Yuanyuan and Noels,
                    Heidi and Akhtar, Shamima and Zhou, Zhe and Koenen, Rory
                    R. and Heyll, Kathrin and Gremse, Felix and Kiessling,
                    Fabian and Grommes, Jochen and Weber, Christian and
                    Schober, Andreas},
  Title           = {{MicroRNA}-155 promotes atherosclerosis by repressing
                    Bcl6 in macrophages},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2012},
  DOI             = {10.1172/jci61716},
  Number          = {11},
  Pages           = {4190--4202},
  ShortJournal    = {JCI},
  Volume          = {122}
}

@Article{Neumann2004,
  Author          = {Neumann, Ulf P. and Berg, Thomas and Bahra, Marcus and
                    Seehofer, Daniel and Langrehr, Jan M. and Neuhaus, Ruth
                    and Radke, Cornelia and Neuhaus, Peter},
  Title           = {Fibrosis progression after liver transplantation in
                    patients with recurrent hepatitis C},
  JournalTitle    = {J. Hepatol.},
  Date            = {2004},
  DOI             = {10.1016/j.jhep.2004.06.029},
  Keywords        = {Neumann-Selection},
  Number          = {5},
  Pages           = {830--836},
  Volume          = {41}
}

@Article{Neumann:166442,
  Author          = {Neumann, Ulf P. and Thelen, Armin and Röcken, Christoph
                    and Seehofer, Daniel and Bahra, Marcus and Riess, Hanno
                    and Jonas, Sven and Schmeding, Maximilian and Pratschke,
                    Johann and Bova, Roberta and Neuhaus, Peter},
  Title           = {Nonresponse to pre-operative chemotherapy does not
                    preclude long-term survival after liver resection in
                    patients with colorectal liver metastases},
  JournalTitle    = {Surgery},
  Date            = {2009},
  DOI             = {10.1016/j.surg.2009.02.004},
  Keywords        = {Neumann-Selection},
  Number          = {1},
  Pages           = {52--59},
  Volume          = {146}
}

@Article{Nevzorova2013,
  Author          = {Nevzorova, Yulia A. and Hu, Wei and Cubero, Francisco J.
                    and Haas, Ute and Freimuth, Julia and Tacke, Frank and
                    Trautwein, Christian and Liedtke, Christian},
  Title           = {Overexpression of c-myc in hepatocytes promotes
                    activation of hepatic stellate cells and facilitates the
                    onset of liver fibrosis},
  JournalTitle    = {Biochimica et Biophysica Acta (BBA) - Molecular Basis of
                    Disease},
  Date            = {2013},
  DOI             = {10.1016/j.bbadis.2013.06.001},
  Keywords        = {Liedtke-Selection,Nevzorova-Selection},
  Number          = {10},
  Pages           = {1765--1775},
  Volume          = {1832}
}

@Article{Nevzorova:134016,
  Author          = {Nevzorova, Yulia A. and Tschaharganeh, Darjus and
                    Gassler, Nikolaus and Geng, Yan and Weiskirchen, Ralf and
                    Sicinski, Piotr and Trautwein, Christian and Liedtke,
                    Christian},
  Title           = {Aberrant Cell Cycle Progression and Endoreplication in
                    Regenerating Livers of Mice That Lack a Single E-Type
                    Cyclin},
  JournalTitle    = {Gastroenterology},
  Date            = {2009},
  DOI             = {10.1053/j.gastro.2009.05.003},
  Keywords        = {Liedtke-Selection,Nevzorova-Selection},
  Number          = {2},
  Pages           = {691--703.e6},
  Subtitle        = {Basic: Liver, Pancreas, and Biliary Tract},
  Volume          = {137}
}

@Article{Nevzorova:193299,
  Author          = {Nevzorova, Yulia A. and Bangen, Jörg-Martin and Hu, Wei
                    and Haas, Ute and Weiskirchen, Ralf and Gassler, Nikolaus
                    and Huss, Sebastian and Tacke, Frank and Sicinski, Piotr
                    and Trautwein, Christian and Liedtke, Christian},
  Title           = {Cyclin E1 controls proliferation of hepatic stellate
                    cells and is essential for liver fibrogenesis in mice},
  JournalTitle    = {Hepatology},
  Date            = {2012},
  DOI             = {10.1002/hep.25736},
  Keywords        = {Liedtke-Selection,Nevzorova-Selection},
  Number          = {3},
  Pages           = {1140--1149},
  Volume          = {56}
}

@Article{Nevzorova:684995,
  Author          = {Nevzorova, Yulia A. and Cubero, Francisco J. and Hu, Wei
                    and Hao, Fengjie and Haas, Ute and Ramadori, Pierluigi
                    and Gassler, Nikolaus and Hoss, Mareike and Strnad, Pavel
                    and Zimmermann, Henning W. and Tacke, Frank and
                    Trautwein, Christian and Liedtke, Christian},
  Title           = {Enhanced expression of c-myc in hepatocytes promotes
                    initiation and progression of alcoholic liver disease},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2015.11.005},
  ids             = {nevzorova2016a},
  Keywords        = {Nevzorova-Selection},
  Number          = {3},
  Pages           = {628--640},
  Volume          = {64}
}

@Article{Nevzorova:716355,
  Author          = {Nevzorova, Yulia A. and Grossmann, Johannes and
                    Trautwein, Christian},
  Title           = {Anti-tumorigenic and anti-angiogenic effects of natural
                    conifer Abies sibirica terpenoids in vivo and in vitro},
  JournalTitle    = {Biomed. Pharmacother.},
  Date            = {2017},
  DOI             = {10.1016/j.biopha.2017.02.035},
  Keywords        = {Nevzorova-Selection},
  Pages           = {386--395},
  Volume          = {89}
}

@Article{Nguyen2020-co,
  Author          = {Nguyen, Long H and Örtqvist, Anne K and Cao, Yin and
                    Simon, Tracey G and Roelstraete, Bjorn and Song, Mingyang
                    and Joshi, Amit D and Staller, Kyle and Chan, Andrew T
                    and Khalili, Hamed and Olén, Ola and Ludvigsson, Jonas
                    F},
  Title           = {Antibiotic use and the development of inflammatory bowel
                    disease: {A} national case-control study in {Sweden}},
  JournalTitle    = {Lancet Gastroenterol. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/s2468-1253(20)30267-3},
  Number          = {11},
  Pages           = {986--995},
  Volume          = {5}
}

@Article{Nguyen2007-lo,
  Author          = {Nguyen, M T Audrey and Favelyukis, Svetlana and Nguyen,
                    Anh-Khoi and Reichart, Donna and Scott, Peter A and Jenn,
                    Alan and Liu-Bryan, Ru and Glass, Christopher K and
                    Neels, Jaap G and Olefsky, Jerrold M},
  Title           = {A subpopulation of macrophages infiltrates hypertrophic
                    adipose tissue and is activated by free fatty acids via
                    Toll-like receptors 2 and 4 and {JNK-dependent}
                    pathways},
  JournalTitle    = {J. Biol. Chem.},
  Date            = {2007},
  DOI             = {10.1074/jbc.M706762200},
  Number          = {48},
  Pages           = {35279--35292},
  Volume          = {282}
}

@Article{Noels2021-pq,
  Author          = {Noels, Heidi and Lehrke, Michael and Vanholder, Raymond
                    and Jankowski, Joachim},
  Title           = {Lipoproteins and fatty acids in chronic kidney disease:
                    {Molecular} and metabolic alterations},
  JournalTitle    = {Nat. Rev. Nephrol.},
  Date            = {2021},
  DOI             = {10.1038/s41581-021-00423-5},
  Keywords        = {Jankowski-Selection,Noels-Selection},
  Number          = {8},
  Pages           = {528--542},
  Volume          = {17}
}

@Article{Noels:234734,
  Author          = {Noels, Heidi and Zhou, Baixue and Tilstam, Pathricia V.
                    and Theelen, Wendy and Li, Xiaofeng and Pawig, Lukas and
                    Schmitz, Corinna and Akhtar, Shamima and Simsekyilmaz,
                    Sakine and Shagdarsuren, Erdenechimeg and Schober,
                    Andreas and Adams, Ralf H. and Bernhagen, Jürgen and
                    Liehn, Elisa A. and Döring, Yvonne and Weber,
                    Christian},
  Title           = {Deficiency of Endothelial Cxcr4 Reduces
                    Reendothelialization and Enhances Neointimal Hyperplasia
                    After Vascular Injury in Atherosclerosis-Prone Mice},
  JournalTitle    = { Arterioscl. Throm. Vas.},
  Date            = {2014},
  DOI             = {10.1161/atvbaha.113.302878},
  Number          = {6},
  Pages           = {1209--1220},
  Volume          = {34}
}

@Article{Noels:753920,
  Author          = {Noels, Heidi and Theelen, Wendy and Sternkopf, Marieke
                    and Jankowski, Vera and Moellmann, Julia and Kraemer,
                    Sandra and Lehrke, Michael and Marx, Nikolaus and Martin,
                    Lukas and Marx, Gernot and Jankowski, Joachim and
                    Goetzenich, Andreas and Stoppe, Christian},
  Title           = {Reduced post-operative {DPP4} activity associated with
                    worse patient outcome after cardiac surgery},
  JournalTitle    = {Sci. Rep.},
  Date            = {2018},
  DOI             = {10.1038/s41598-018-30235-w},
  Keywords        = {Noels-Selection},
  Number          = {1},
  Pages           = {11820},
  Volume          = {8}
}

@Article{Oberbach2017,
  Author          = {Oberbach, Andreas and Haange, Sven-Bastiaan and
                    Schlichting, Nadine and Heinrich, Marco and Lehmann,
                    Stefanie and Till, Holger and Hugenholtz, Floor and
                    Kullnick, Yvonne and Smidt, Hauke and Frank, Karin and
                    Seifert, Jana and Jehmlich, Nico and von Bergen, Martin},
  Title           = {Metabolic in Vivo Labeling Highlights Differences of
                    Metabolically Active Microbes from the Mucosal
                    Gastrointestinal Microbiome between High-Fat and Normal
                    Chow Diet},
  JournalTitle    = {J. Proteome Res.},
  Date            = {2017},
  DOI             = {10.1021/acs.jproteome.6b00973},
  Keywords        = {von Bergen-Selection},
  Number          = {4},
  Pages           = {1593--1604},
  Volume          = {16}
}

@Article{Odajima2016-sb,
  Author          = {Odajima, Junko and Saini, Siddharth and Jung, Piotr and
                    Ndassa-Colday, Yasmine and Ficaro, Scott and Geng, Yan
                    and Marco, Eugenio and Michowski, Wojciech and Wang,
                    Yaoyu E. and DeCaprio, James A. and Litovchick, Larisa
                    and Marto, Jarrod and Sicinski, Piotr},
  Title           = {Proteomic Landscape of Tissue-Specific Cyclin E
                    Functions in Vivo},
  JournalTitle    = {PLoS Genet.},
  Date            = {2016},
  DOI             = {10.1371/journal.pgen.1006429},
  Number          = {11},
  Pages           = {e1006429},
  Volume          = {12}
}

@Article{Ohl:729725,
  Author          = {Ohl, Kim and Fragoulis, Athanassios and Klemm, Patricia
                    and Baumeister, Julian and Klock, Wiebke and Verjans, Eva
                    and Böll, Svenja and Möllmann, Julia and Lehrke,
                    Michael and Costa, Ivan and Denecke, Bernd and Schippers,
                    Angela and Roth, Johannes and Wagner, Norbert and Wruck,
                    Christoph and Tenbrock, Klaus},
  Title           = {Nrf2 Is a Central Regulator of Metabolic Reprogramming
                    of Myeloid-Derived Suppressor Cells in Steady State and
                    Sepsis},
  JournalTitle    = {Front. Immunol.},
  Date            = {2018},
  DOI             = {10.3389/fimmu.2018.01552},
  Pages           = {1552},
  Volume          = {9}
}

@Article{OldeDamink2002,
  Author          = {Olde Damink, Steven W. M. and Jalan, Rajiv and Redhead,
                    Doris N. and Hayes, Peter C. and Deutz, Nicolaas E. P.
                    and Soeters, Peter B.},
  Title           = {Interorgan ammonia and amino acid metabolism in
                    metabolically stable patients with cirrhosis and a
                    {TIPSS}},
  JournalTitle    = {Hepatology},
  Date            = {2002},
  DOI             = {10.1053/jhep.2002.36497},
  Number          = {5},
  Pages           = {1163--1171},
  Subtitle        = {Interorgan ammonia and amino acid metabolism in
                    metabolically stable patients with cirrhosis and a
                    TIPSS},
  Volume          = {36}
}

@Article{OldeDamink2007,
  Author          = {Olde Damink, Steven W. M. and Jalan, Rajiv and Deutz,
                    Nicolaas E. P. and Dejong, Cornelis H. C. and Redhead,
                    Doris N. and Hynd, Paula and Hayes, Peter C. and Soeters,
                    Peter B.},
  Title           = {Isoleucine infusion during “simulated” upper
                    gastrointestinal bleeding improves liver and muscle
                    protein synthesis in cirrhotic patients},
  JournalTitle    = {Hepatology},
  Date            = {2007},
  DOI             = {10.1002/hep.21463},
  Number          = {3},
  Pages           = {560--568},
  Volume          = {45}
}

@Article{OldeDamink2008,
  Author          = {Olde Damink, Steven W.M. and Jalan, Rajiv and Deutz,
                    Nicolaas E.P. and Hayes, Peter C. and Soeters, Peter B.},
  Title           = {Protein synthesis is severely diminished following a
                    simulated upper {GI} bleed in patients with cirrhosis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2008},
  DOI             = {10.1016/j.jhep.2008.04.018},
  Number          = {5},
  Pages           = {726--731},
  Volume          = {49}
}

@Article{Olivo_Pimentel2020-br,
  Author          = {Olivo Pimentel, Verónica and Yaromina, Ala and Marcus,
                    Damiënne and Dubois, Ludwig J. and Lambin, Philippe},
  Title           = {A novel co-culture assay to assess anti-tumor {CD8+} T
                    cell cytotoxicity via luminescence and multicolor flow
                    cytometry},
  JournalTitle    = {J. Immunol. Methods},
  Date            = {2020},
  DOI             = {10.1016/j.jim.2020.112899},
  Keywords        = {Co-culture assay; Cytotoxic T cells; Ex vivo; Flow
                    cytometry; Luciferase assay; Tumor cells},
  Number          = {112899},
  Pages           = {112899},
  Volume          = {487}
}

@Article{Olthof2017,
  Author          = {Olthof, P B and Huisman, F and Schaap, F. G. and van
                    Lienden, K P and Bennink, R J and van Golen, R F and
                    Heger, M and Verheij, J and Jansen, P L and Olde Damink,
                    S. W. and van Gulik, T M},
  Title           = {Effect of obeticholic acid on liver regeneration
                    following portal vein embolization in an experimental
                    model},
  JournalTitle    = {Br. J. Surg.},
  Date            = {2017},
  DOI             = {10.1002/bjs.10466},
  Number          = {5},
  Pages           = {590--599},
  Volume          = {104}
}

@Article{Opacic:722659,
  Author          = {Opacic, Tatjana and Dencks, Stefanie and Theek, Benjamin
                    and Piepenbrock, Marion and Ackermann, Dimitri and Rix,
                    Anne and Lammers, Twan and Stickeler, Elmar and Delorme,
                    Stefan and Schmitz, Georg and Kiessling, Fabian},
  Title           = {Motion model ultrasound localization microscopy for
                    preclinical and clinical multiparametric tumor
                    characterization},
  JournalTitle    = {Nat. Commun.},
  Date            = {2018},
  DOI             = {10.1038/s41467-018-03973-8},
  Keywords        = {Kießling-Selection},
  Number          = {1},
  Pages           = {1527},
  Volume          = {9}
}

@Article{Orth-Alampour2021-pm,
  Author          = {Orth-Alampour, Setareh and Gayrard, Nathalie and Salem,
                    Silvia and Bhargava, Shruti and Jankowski, Vera and
                    Jover, Bernard and Notarnicola, Cécile and Noels, Heidi
                    and van der Vorst, Emiel P C and Kuppe, Christoph and
                    Wolf, Michael and Goettsch, Claudia and Theelen, Wendy
                    and Bruck, Heike and Fliser, Danilo and Loscalzo, Joseph
                    and Wu, Zhuojun and Marx, Nikolaus and Zidek, Walter and
                    Argilés, Àngel and Jankowski, Joachim},
  Title           = {Prevention of vascular calcification by the endogenous
                    chromogranin A-derived mediator that inhibits osteogenic
                    transdifferentiation},
  JournalTitle    = {Basic Res. Cardiol.},
  Addendum        = preliminarywork,
  Date            = {2021},
  DOI             = {10.1007/s00395-021-00899-z},
  Keywords        = {Jankowski-Selection},
  Number          = {1},
  Pages           = {57},
  Volume          = {116}
}

@Article{Osada2008,
  Author          = {Osada, Takuya and Chong, Gabriel and Tansik, Robert and
                    Hong, Timothy and Spector, Neil and Kumar, Rakesh and
                    Hurwitz, Herbert I. and Dev, Inderjit and Nixon, Andrew
                    B. and Lyerly, H. Kim and Clay, Timothy and Morse,
                    Michael A.},
  Title           = {The effect of anti-{VEGF} therapy on immature myeloid
                    cell and dendritic cells in cancer patients},
  JournalTitle    = {Cancer Immunol. Immunother.},
  Date            = {2008},
  DOI             = {10.1007/s00262-007-0441-x},
  Number          = {8},
  Pages           = {1115--1124},
  Volume          = {57}
}

@Article{Osaki1998-kk,
  Author          = {Osaki, T and Péron, J M and Cai, Q and Okamura, H and
                    Robbins, P D and Kurimoto, M and Lotze, M T and Tahara,
                    H},
  Title           = {{IFN-gamma-inducing} {factor/IL-18} administration
                    mediates {IFN-gamma-} and {IL-12-independent} antitumor
                    effects},
  JournalTitle    = {J. Immunol.},
  Date            = {1998},
  Number          = {4},
  Pages           = {1742--1749},
  Volume          = {160}
}

@Article{Osterman2015Regulation,
  Author          = {Osterman, I. A. and Dikhtyar, Yu. Yu. and Bogdanov, A.
                    A. and Dontsova, O. A. and Sergiev, P. V.},
  Title           = {Regulation of flagellar gene expression in Bacteria},
  JournalTitle    = {Biochemistry (Moscow)},
  Date            = {2015-11},
  DOI             = {10.1134/s000629791511005x},
  Number          = {11},
  Pages           = {1447--1456},
  Volume          = {80}
}

@Article{Otto2021-jh,
  Author          = {Otto, Natasja A. and Butler, Joe M. and Ramirez-Moral,
                    Ivan and van Weeghel, Michel and van Heijst, Jeroen W. J.
                    and Scicluna, Brendon P. and Houtkooper, Riekelt H. and
                    de Vos, Alex F. and van der Poll, Tom},
  Title           = {Adherence Affects Monocyte Innate Immune Function and
                    Metabolic Reprogramming after Lipopolysaccharide
                    Stimulation In Vitro},
  JournalTitle    = {J. Immunol.},
  Date            = {2021},
  DOI             = {10.4049/jimmunol.2000702},
  Number          = {4},
  Pages           = {827--838},
  Volume          = {206}
}

@Article{Ozdirik2021-sp,
  Author          = {Özdirik, Burcin and Müller, Tobias and Wree, Alexander
                    and Tacke, Frank and Sigal, Michael},
  Title           = {The role of Microbiota in primary sclerosing cholangitis
                    and related biliary malignancies},
  JournalTitle    = {Int. J. Mol. Sci.},
  Addendum        = preliminarywork,
  Date            = {2021},
  DOI             = {10.3390/ijms22136975},
  Keywords        = {cholangiocellular carcinoma; gut-liver axis; microbiome;
                    microbiota; primary sclerosing cholangitis},
  Number          = {13},
  Pages           = {6975},
  Volume          = {22}
}

@Article{Pabst:780352,
  Author          = {Pabst, Oliver and Slack, Emma},
  Title           = {IgA and the intestinal microbiota},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2020},
  DOI             = {10.1038/s41385-019-0227-4},
  ids             = {Pabst2020IgA},
  Keywords        = {,CRC1382-Project B06,CRC1382-Project Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {12--21},
  Subtitle        = {The importance of being specific},
  Volume          = {13}
}

@Article{Pabst:836427,
  Author          = {Pabst, Oliver and Izcue, Ana},
  Title           = {Secretory IgA},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1038/s41575-021-00563-w},
  ids             = {pabst2022a},
  Keywords        = {Izcue-Selection,CRC1382-Project B06,CRC1382-Project
                    Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {2 Seiten},
  Subtitle        = {Controlling the gut microbiota}
}

@Article{Palmer2007-kr,
  Author          = {Palmer, Chana and Bik, Elisabeth M and DiGiulio, Daniel
                    B and Relman, David A and Brown, Patrick O},
  Title           = {Development of the Human Infant Intestinal Microbiota},
  JournalTitle    = {PLoS Biol.},
  Date            = {2007},
  DOI             = {10.1371/journal.pbio.0050177},
  Number          = {7},
  Pages           = {e177},
  Volume          = {5}
}

@Article{Palmowski:164420,
  Author          = {Palmowski, Moritz and Huppert, Jochen and Hauff, Peter
                    and Reinhardt, Michael and Schreiner, Karin and Socher,
                    Michaela A. and Hallscheidt, Peter and Kauffmann, Guenter
                    W. and Semmler, Wolfhard and Kiessling, Fabian},
  Title           = {Vessel Fractions in Tumor Xenografts Depicted by Flow-
                    or Contrast-Sensitive Three-Dimensional High-Frequency
                    {Doppler} Ultrasound Respond Differently to
                    Antiangiogenic Treatment},
  JournalTitle    = {Cancer Res.},
  Date            = {2008},
  DOI             = {10.1158/0008-5472.can-08-0285},
  Keywords        = {Kießling-Selection},
  Number          = {17},
  Pages           = {7042--7049},
  Volume          = {68}
}

@Article{Park2019-po,
  Author          = {Park, Jieun and Levic, Daniel S. and Sumigray, Kaelyn D.
                    and Bagwell, Jennifer and Eroglu, Oznur and Block, Carina
                    L. and Eroglu, Cagla and Barry, Robert and Lickwar, Colin
                    R. and Rawls, John F. and Watts, Stephen A. and Lechler,
                    Terry and Bagnat, Michel},
  Title           = {Lysosome-Rich Enterocytes Mediate Protein Absorption in
                    the Vertebrate Gut},
  JournalTitle    = {Dev. Cell},
  Date            = {2019},
  DOI             = {10.1016/j.devcel.2019.08.001},
  Keywords        = {Cubilin; Dab2; inter-organ transport; intestine;
                    kwashiorkor; lysosome-rich enterocytes (LREs);
                    malnutrition; mouse; protein absorption; zebrafish},
  Number          = {1},
  Pages           = {7--20.e6},
  Volume          = {51}
}

@Article{Pastor-Arroyo2020-wj,
  Author          = {Pastor-Arroyo, Eva M and Knöpfel, Thomas and Imenez
                    Silva, Pedro H and Schnitzbauer, Udo and Poncet, Nadège
                    and Biber, Jürg and Wagner, Carsten A and Hernando,
                    Nati},
  Title           = {Intestinal epithelial ablation of {Pit-2/Slc20a2} in
                    mice leads to sustained elevation of vitamin {D3} upon
                    dietary restriction of phosphate},
  JournalTitle    = {Acta Physiol. (Oxf.)},
  Date            = {2020},
  DOI             = {10.1111/apha.13526},
  Keywords        = {Slc20; Slc34; intestinal absorption; phosphate; vitamin
                    D3},
  Number          = {2},
  Pages           = {e13526},
  Volume          = {230}
}

@Article{Pean2013-xc,
  Author          = {Péan, Noémie and Doignon, Isabelle and Garcin,
                    Isabelle and Besnard, Aurore and Julien, Boris and Liu,
                    Bingkaı̈ and Branchereau, Sophie and Spraul, Anne and
                    Guettier, Catherine and Humbert, Lydie and Schoonjans,
                    Kristina and Rainteau, Dominique and Tordjmann, Thierry},
  Title           = {The receptor {TGR5} protects the liver from bile acid
                    overload during liver regeneration in mice},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26463},
  Number          = {4},
  Pages           = {1451--1460},
  Volume          = {58}
}

@Article{Peiseler2022-sw,
  Author          = {Peiseler, Moritz and Schwabe, Robert and Hampe, Jochen
                    and Kubes, Paul and Heikenwälder, Mathias and Tacke,
                    Frank},
  Title           = {Immune mechanisms linking metabolic injury to
                    inflammation and fibrosis in fatty liver disease –
                    novel insights into cellular communication circuits},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jhep.2022.06.012},
  Number          = {4},
  Pages           = {1136--1160},
  Volume          = {77}
}

@Article{Peiseler:815753,
  Author          = {Peiseler, Moritz and Tacke, Frank},
  Title           = {Inflammatory Mechanisms Underlying Nonalcoholic
                    Steatohepatitis and the Transition to Hepatocellular
                    Carcinoma},
  JournalTitle    = {Cancers (Basel)},
  Date            = {2021},
  DOI             = {10.3390/cancers13040730},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {730},
  Volume          = {13}
}

@Article{Peiseler:828489,
  Author          = {Peiseler, Moritz and Tacke, Frank},
  Title           = {An Unexpected Line of Defense},
  JournalTitle    = {Hepatology},
  Date            = {2021},
  DOI             = {10.1002/hep.31895},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {5},
  Pages           = {2888--2890},
  Subtitle        = {Hepatoprotective Eosinophils in Ischemia‐Reperfusion
                    Injury},
  Volume          = {74}
}

@Article{Pellicoro2014,
  Author          = {Pellicoro, Antonella and Ramachandran, Prakash and
                    Iredale, John P. and Fallowfield, Jonathan A.},
  Title           = {Liver fibrosis and repair: {Immune} regulation of wound
                    healing in a solid organ},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2014},
  DOI             = {10.1038/nri3623},
  Keywords        = {Animals; Dendritic Cells; Fibrosis; Hepatic Stellate
                    Cells; Humans; Inflammation; Liver; Liver Cirrhosis;
                    Macrophages; Mice; Myofibroblasts; Natural Killer
                    T-Cells; T-Lymphocytes,Regulatory; Th1 Cells; Th17 Cells;
                    Th2 Cells; Wound Healing},
  Number          = {3},
  Pages           = {181--194},
  Volume          = {14}
}

@Article{Pereira:803881,
  Author          = {Pereira, Fátima C. and Wasmund, Kenneth and Cobankovic,
                    Iva and Jehmlich, Nico and Herbold, Craig W. and Lee,
                    Kang Soo and Sziranyi, Barbara and Vesely, Cornelia and
                    Decker, Thomas and Stocker, Roman and Warth, Benedikt and
                    von Bergen, Martin and Wagner, Michael and Berry, David},
  Title           = {Rational design of a microbial consortium of mucosal
                    sugar utilizers reduces Clostridiodes difficile
                    colonization},
  JournalTitle    = {Nat. Commun.},
  Date            = {2020},
  DOI             = {10.1038/s41467-020-18928-1},
  Keywords        = {,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {5104},
  Volume          = {11}
}

@Article{Perino2021-ua,
  Author          = {Perino, Alessia and Demagny, Hadrien and
                    Velazquez-Villegas, Laura and Schoonjans, Kristina},
  Title           = {Molecular Physiology of Bile Acid Signaling in Health,
                    Disease, and Aging},
  JournalTitle    = {Physiol. Rev.},
  Date            = {2021},
  DOI             = {10.1152/physrev.00049.2019},
  Keywords        = {FXR; NAFLD; TGR5; metabolic syndrome; microbiome},
  Number          = {2},
  Pages           = {683--731},
  Volume          = {101}
}

@Article{Peterson2007IgA,
  Author          = {Peterson, Daniel A. and McNulty, Nathan P. and Guruge,
                    Janaki L. and Gordon, Jeffrey I.},
  Title           = {{IgA} Response to Symbiotic Bacteria as a Mediator of
                    Gut Homeostasis},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2007-11},
  DOI             = {10.1016/j.chom.2007.09.013},
  Number          = {5},
  Pages           = {328--339},
  Volume          = {2}
}

@Article{Petra2021-yq,
  Author          = {Petra, Eleni and He, Tianlin and Lygirou, Vasiliki and
                    Latosinska, Agnieszka and Mischak, Harald and Vlahou,
                    Antonia and Jankowski, Joachim},
  Title           = {Urine peptidome analysis in cardiorenal syndrome
                    reflects molecular processes},
  JournalTitle    = {Sci. Rep.},
  Date            = {2021},
  DOI             = {10.1038/s41598-021-95695-z},
  Keywords        = {Jankowski-Selection},
  Number          = {1},
  Pages           = {16219},
  Volume          = {11}
}

@Article{Petruschke2021-zx,
  Author          = {Petruschke, Hannes and Schori, Christian and Canzler,
                    Sebastian and Riesbeck, Sarah and Poehlein, Anja and
                    Daniel, Rolf and Frei, Daniel and Segessemann, Tina and
                    Zimmerman, Johannes and Marinos, Georgios and Kaleta,
                    Christoph and Jehmlich, Nico and Ahrens, Christian H and
                    von Bergen, Martin},
  Title           = {Discovery of novel community-relevant small proteins in
                    a simplified human intestinal microbiome},
  JournalTitle    = {Microbiome},
  Date            = {2021},
  DOI             = {10.1186/s40168-020-00981-z},
  Keywords        = {von Bergen-Selection},
  Number          = {1},
  Pages           = {55},
  Volume          = {9}
}

@Article{Phan2020-ks,
  Author          = {Phan, An N T and Blank, Lars M.},
  Title           = {{GC-MS-based} metabolomics for the smut fungus Ustilago
                    maydis: A comprehensive method optimization to quantify
                    intracellular metabolites},
  JournalTitle    = {Front. Mol. Biosci.},
  Date            = {2020},
  DOI             = {10.3389/fmolb.2020.00211},
  Keywords        = {Blank-Selection},
  Pages           = {211},
  Volume          = {7}
}

@Article{Pieper:812434,
  Author          = {Pieper, Robert and van Best, Niels and van Vorst, Kira
                    and Ebner, Friederike and Reissmann, Monika and Hornef,
                    Mathias W. and Fulde, Marcus},
  Title           = {Toward a porcine in vivo model to analyze the
                    pathogenesis of {TLR}5-dependent enteropathies},
  JournalTitle    = {Gut microbes},
  Date            = {2020},
  DOI             = {10.1080/19490976.2020.1782163},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {1782163},
  Volume          = {12}
}

@Article{Pollheimer2015-wn,
  Author          = {Pollheimer, Marion J and Fickert, Peter},
  Title           = {Animal models in primary biliary cirrhosis and primary
                    sclerosing cholangitis},
  JournalTitle    = {Clin. Rev. Allergy Immunol.},
  Date            = {2015},
  DOI             = {10.1007/s12016-014-8442-y},
  Number          = {2-3},
  Pages           = {207--217},
  Volume          = {48}
}

@Article{Pott2011,
  Author          = {Pott, Johanna and Mahlakõiv, Tanel and Mordstein,
                    Markus and Duerr, Claudia U. and Michiels, Thomas and
                    Stockinger, Silvia and Staeheli, Peter and Hornef,
                    Mathias W.},
  Title           = {{IFN}-λ determines the intestinal epithelial antiviral
                    host defense},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2011},
  DOI             = {10.1073/pnas.1100552108},
  Keywords        = {Hornef-Selection},
  Number          = {19},
  Pages           = {7944--7949},
  Volume          = {108}
}

@Article{Agrawal2021-iv,
  Author          = {Agrawal, Manasi and Sabino, João and Frias-Gomes,
                    Catarina and Hillenbrand, Christen M. and Soudant, Celine
                    and Axelrad, Jordan E. and Shah, Shailja C. and
                    Ribeiro-Mourão, Francisco and Lambin, Thomas and Peter,
                    Inga and Colombel, Jean-Frederic and Narula, Neeraj and
                    Torres, Joana},
  Title           = {Early life exposures and the risk of inflammatory bowel
                    disease: {Systematic} review and meta-analyses},
  JournalTitle    = {EClinicalMedicine},
  Date            = {2021},
  DOI             = {10.1016/j.eclinm.2021.100884},
  Number          = {100884},
  Volume          = {36}
}

@Article{Pott2012a,
  Author          = {Pott, Johanna and Stockinger, Silvia and Torow, Natalia
                    and Smoczek, Anna and Lindner, Cornelia and McInerney,
                    Gerald and Bäckhed, Fredrik and Baumann, Ulrich and
                    Pabst, Oliver and Bleich, André and Hornef, Mathias W.},
  Title           = {Age-Dependent {TLR3} Expression of the Intestinal
                    Epithelium Contributes to Rotavirus Susceptibility},
  JournalTitle    = {PLoS Pathog.},
  Date            = {2012},
  DOI             = {10.1371/journal.ppat.1002670},
  ids             = {pott2012-ao,Pott2012-ao},
  Number          = {5},
  Pages           = {e1002670},
  Type            = {PLoS Pathog 8:e1002670.},
  Volume          = {8}
}

@Article{Puengel2022-id,
  Author          = {Puengel, Tobias and Lefere, Sander and Hundertmark, Jana
                    and Kohlhepp, Marlene and Penners, Christian and Van de
                    Velde, Frederique and Lapauw, Bruno and Hoorens, Anne and
                    Devisscher, Lindsey and Geerts, Anja and Boehm, Stephanie
                    and Zhao, Qihong and Krupinski, John and Charles, Edgar
                    D. and Zinker, Bradley and Tacke, Frank},
  Title           = {Combined Therapy with a {CCR2/CCR5} Antagonist and
                    {FGF21} Analogue Synergizes in Ameliorating
                    Steatohepatitis and Fibrosis},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2022},
  DOI             = {10.3390/ijms23126696},
  Number          = {12},
  Pages           = {6696},
  Volume          = {23}
}

@Article{Puengel:791898,
  Author          = {Puengel, Tobias and De Vos, Steve and Hundertmark, Jana
                    and Kohlhepp, Marlene and Guldiken, Nurdan and Pujuguet,
                    Philippe and Auberval, Marielle and Marsais, Florence and
                    Shoji, Kenji F. and Saniere, Laurent and Trautwein,
                    Christian and Lüdde, Tom and Strnad, Pavel and Brys,
                    Reginald and Clément-Lacroix, Philippe and Tacke,
                    Frank},
  Title           = {The Medium-Chain Fatty Acid Receptor {GPR}84 Mediates
                    Myeloid Cell Infiltration Promoting Steatohepatitis and
                    Fibrosis},
  JournalTitle    = {J. Clin. Med.},
  Date            = {2020},
  DOI             = {10.3390/jcm9041140},
  ids             = {Puengel:791898a},
  Keywords        = {,CRC1382-Project A03,CRC1382-Project A01,CRC1382-Project
                    A03,CRC1382-Project B05,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {1140},
  Volume          = {9}
}

@Article{Puengel:828593,
  Author          = {Puengel, Tobias and Tacke, Frank},
  Title           = {Editorial: prevalence, progression rates and mortality
                    predictors of non-alcoholic fatty liver disease reflected
                    by German statutory health insurance data},
  JournalTitle    = {Aliment. Pharmacol. Ther.},
  Date            = {2020},
  DOI             = {10.1111/apt.16077},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {8},
  Pages           = {1412--1413},
  Volume          = {52}
}

@Article{Puengel:839874,
  Author          = {Puengel, Tobias and Weber, Beate and Wirtz, Theresa H.
                    and Buendgens, Lukas and Loosen, Sven H. and Geisler,
                    Lukas and Özdirik, Burcin and Karim, Hamesch and
                    Jhaisha, Samira Abu and Brozat, Jonathan F. and
                    Hohlstein, Philipp and Eisert, Albrecht and Yagmur, Eray
                    and Trautwein, Christian and Tacke, Frank and Koch,
                    Alexander},
  Title           = {Low Serum Levels of Soluble Receptor Activator of
                    Nuclear Factor κ B Ligand (s{RANKL}) Are Associated with
                    Metabolic Dysregulation and Predict Long-Term Mortality
                    in Critically Ill Patients},
  JournalTitle    = {Diagnostics},
  Date            = {2022},
  DOI             = {10.3390/diagnostics12010062},
  Keywords        = {,CRC1382-Project B05,CRC1382-Project A06,CRC1382-Project
                    A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {62},
  Volume          = {12}
}

@Article{Queck:813493,
  Author          = {Queck, Alexander and Bode, Hannah and Uschner, Frank E.
                    and Brol, Maximilian J. and Graf, Christiana and Schulz,
                    Martin and Jansen, Christian and Praktiknjo, Michael and
                    Schierwagen, Robert and Klein, Sabine and Trautwein,
                    Christian and Wasmuth, Hermann E. and Berres, Marie-Luise
                    and Trebicka, Jonel and Lehmann, Jennifer},
  Title           = {Systemic {MCP}-1 Levels Derive Mainly From Injured Liver
                    and Are Associated With Complications in Cirrhosis},
  JournalTitle    = {Front. Immunol.},
  Date            = {2020},
  DOI             = {10.3389/fimmu.2020.00354},
  Keywords        = {,CRC1382-Project B04,CRC1382-Project A09,CRC1382-Project
                    A06,CRC1382-Project A08,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {354},
  Volume          = {11}
}

@Article{Queck:815756,
  Author          = {Queck, Alexander and Thomas, Dominique and Jansen,
                    Christian and Schreiber, Yannick and Rüschenbaum,
                    Sabrina and Praktiknjo, Michael and Schwarzkopf,
                    Katharina Maria and Mücke, Marcus Maximilian and
                    Schierwagen, Robert and Uschner, Frank Erhard and Meyer,
                    Carsten and Clària, Joan and Zeuzem, Stefan and
                    Geisslinger, Gerd and Trebicka, Jonel and Lange,
                    Christian Markus},
  Title           = {Pathophysiological role of prostanoids in coagulation of
                    the portal venous system in liver cirrhosis},
  JournalTitle    = {PLOS ONE},
  Date            = {2019},
  DOI             = {10.1371/journal.pone.0222840},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {10},
  Pages           = {e0222840},
  Volume          = {14}
}

@Article{Sark2022-xw,
  Author          = {Sark, Annelot D. and Fromme, Malin and Olejnicka, Beata
                    and Welte, Tobias and Strnad, Pavel and Janciauskiene,
                    Sabina and Stolk, Jan},
  Title           = {The Relationship between Plasma Alpha-1-Antitrypsin
                    Polymers and Lung or Liver Function in {ZZ}
                    Alpha-1-Antitrypsin-Deficient Patients},
  JournalTitle    = {Biomolecules},
  Date            = {2022},
  DOI             = {10.3390/biom12030380},
  Keywords        = {ELISA; SERPINA1; alpha1-antitrypsin; deficiency; liver
                    biomarkers; lung function; polymers},
  Number          = {3},
  Pages           = {380},
  Volume          = {12}
}

@Article{Roh2018-gx,
  Author          = {Roh, Jong Seong and Sohn, Dong Hyun},
  Title           = {Damage-Associated Molecular Patterns in Inflammatory
                    Diseases},
  JournalTitle    = {Immune Netw.},
  Date            = {2018},
  DOI             = {10.4110/in.2018.18.e27},
  Keywords        = {Damage-associated molecular patterns; Inflammation;
                    Inflammatory diseases; Pattern recognition receptors},
  Number          = {4},
  Pages           = {e27},
  Volume          = {18}
}

@Article{Queck:828617,
  Author          = {Queck, Alexander and Uschner, Frank E. and Ferstl,
                    Philip G. and Schulz, Martin and Brol, Maximilian J. and
                    Praktiknjo, Michael and Schierwagen, Robert and Klein,
                    Sabine and Strassburg, Christian P. and Meyer, Carsten
                    and Jansen, Christian and Berres, Marie-Luise and
                    Trebicka, Jonel},
  Title           = {Role of circulating angiogenin levels in portal
                    hypertension and {TIPS}},
  JournalTitle    = {PLOS ONE},
  Date            = {2021},
  DOI             = {10.1371/journal.pone.0256473},
  Keywords        = {,CRC1382-Project B04,CRC1382-Project A09,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {8},
  Pages           = {e0256473},
  Volume          = {16}
}

@Article{Quinn2020-ii,
  Author          = {Quinn, Robert A and Melnik, Alexey V and Vrbanac, Alison
                    and Fu, Ting and Patras, Kathryn A and Christy, Mitchell
                    P and Bodai, Zsolt and Belda-Ferre, Pedro and Tripathi,
                    Anupriya and Chung, Lawton K and Downes, Michael and
                    Welch, Ryan D and Quinn, Melissa and Humphrey, Greg and
                    Panitchpakdi, Morgan and Weldon, Kelly C and Aksenov,
                    Alexander and da Silva, Ricardo and Avila-Pacheco, Julian
                    and Clish, Clary and Bae, Sena and Mallick, Himel and
                    Franzosa, Eric A and Lloyd-Price, Jason and Bussell,
                    Robert and Thron, Taren and Nelson, Andrew T and Wang,
                    Mingxun and Leszczynski, Eric and Vargas, Fernando and
                    Gauglitz, Julia M and Meehan, Michael J and Gentry, Emily
                    and Arthur, Timothy D and Komor, Alexis C and Poulsen,
                    Orit and Boland, Brigid S and Chang, John T and Sandborn,
                    William J and Lim, Meerana and Garg, Neha and Lumeng,
                    Julie C and Xavier, Ramnik J and Kazmierczak, Barbara I
                    and Jain, Ruchi and Egan, Marie and Rhee, Kyung E and
                    Ferguson, David and Raffatellu, Manuela and Vlamakis,
                    Hera and Haddad, Gabriel G and Siegel, Dionicio and
                    Huttenhower, Curtis and Mazmanian, Sarkis K and Evans,
                    Ronald M and Nizet, Victor and Knight, Rob and
                    Dorrestein, Pieter C},
  Title           = {Global chemical effects of the microbiome include new
                    bile-acid conjugations},
  JournalTitle    = {Nature},
  Date            = {2020},
  DOI             = {10.1038/s41586-020-2047-9},
  Number          = {7797},
  Pages           = {123--129},
  Volume          = {579}
}

@Article{Raczynski2012-ce,
  Author          = {Raczynski, Arkadiusz R and Muthupalani, Sureshkumar and
                    Schlieper, Katherine and Fox, James G and Tannenbaum,
                    Steven R and Schauer, David B},
  Title           = {Enteric infection with Citrobacter rodentium induces
                    coagulative liver necrosis and hepatic inflammation prior
                    to peak infection and colonic disease},
  JournalTitle    = {PLoS One},
  Date            = {2012},
  DOI             = {10.1371/journal.pone.0033099},
  Number          = {3},
  Pages           = {e33099},
  Volume          = {7}
}

@Article{Rai2020-hp,
  Author          = {Rai, Ravi P and Liu, Yunshan and Iyer, Smita S and Liu,
                    Silvia and Gupta, Biki and Desai, Chirayu and Kumar,
                    Pradeep and Smith, Tekla and Singhi, Aatur D and Nusrat,
                    Asma and Parkos, Charles A and Monga, Satdarshan P and
                    Czaja, Mark J and Anania, Frank A and Raeman, Reben},
  Title           = {Blocking integrin $\alpha$4$\beta$7-mediated {CD4} {T}
                    cell recruitment to the intestine and liver protects mice
                    from western diet-induced non-alcoholic steatohepatitis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jhep.2020.05.047},
  Keywords        = {Epithelial barrier; Gut permeability; Inflammation;
                    Microbiota; Non-alcoholic fatty liver disease},
  Number          = {5},
  Pages           = {1013--1022},
  Volume          = {73}
}

@Article{Rama2022-xj,
  Author          = {Rama, Elena and Mohapatra, Saurav Ranjan and Melcher,
                    Christoph and Nolte, Teresa and Dadfar, Seyed Mohammadali
                    and Brueck, Ramona and Pathak, Vertika and Rix, Anne and
                    Gries, Thomas and Schulz, Volkmar and Lammers, Twan and
                    Apel, Christian and Jockenhoevel, Stefan and Kiessling,
                    Fabian},
  Title           = {Monitoring the Remodeling of Biohybrid
                    {Tissue‐Engineered} Vascular Grafts by Multimodal
                    Molecular Imaging},
  JournalTitle    = {Adv. Sci.},
  Date            = {2022},
  DOI             = {10.1002/advs.202105783},
  Keywords        = {Kießling-Selection},
  Number          = {10},
  Pages           = {2105783},
  Volume          = {9}
}

@Article{Reimer:780555,
  Author          = {Reimer, Katharina C. and Wree, Alexander and Roderburg,
                    Christoph and Tacke, Frank},
  Title           = {New drugs for {NAFLD}},
  JournalTitle    = {Hepatol. Int.},
  Date            = {2020},
  DOI             = {10.1007/s12072-019-10001-4},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {8--23},
  Subtitle        = {Lessons from basic models to the clinic},
  Volume          = {14}
}

@Article{Reitmeier:835050,
  Author          = {Reitmeier, Sandra and Hitch, Thomas C. A. and Treichel,
                    Nicole and Fikas, Nikolaos and Hausmann, Bela and
                    Ramer-Tait, Amanda E. and Neuhaus, Klaus and Berry, David
                    and Haller, Dirk and Lagkouvardos, Ilias and Clavel,
                    Thomas},
  Title           = {Handling of spurious sequences affects the outcome of
                    high-throughput 16S r{RNA} gene amplicon profiling},
  JournalTitle    = {ISME communications},
  Date            = {2021},
  DOI             = {10.1038/s43705-021-00033-z},
  Keywords        = {Clavel-Selection,CRC1382-Project A05,CRC1382-Project
                    Q02,CRC1382-Project Q02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {31},
  Volume          = {1}
}

@Article{Remmerie2020-gi,
  Author          = {Remmerie, Anneleen and Martens, Liesbet and Thoné,
                    Tinne and Castoldi, Angela and Seurinck, Ruth and Pavie,
                    Benjamin and Roels, Joris and Vanneste, Bavo and De
                    Prijck, Sofie and Vanhockerhout, Mathias and Binte Abdul
                    Latib, Mushida and Devisscher, Lindsey and Hoorens, Anne
                    and Bonnardel, Johnny and Vandamme, Niels and Kremer,
                    Anna and Borghgraef, Peter and Van Vlierberghe, Hans and
                    Lippens, Saskia and Pearce, Edward and Saeys, Yvan and
                    Scott, Charlotte L.},
  Title           = {Osteopontin Expression Identifies a Subset of Recruited
                    Macrophages Distinct from Kupffer Cells in the Fatty
                    Liver},
  JournalTitle    = {Immunity},
  Date            = {2020},
  DOI             = {10.1016/j.immuni.2020.08.004},
  Keywords        = {Kupffer cells; MAFLD; NAFLD; NASH; Western Diet; lipid;
                    liver; macrophages; subsets},
  Number          = {3},
  Pages           = {641--657.e14},
  Volume          = {53}
}

@Article{Rennert2015-gv,
  Author          = {Rennert, Knut and Steinborn, Sandra and Gröger, Marko
                    and Ungerböck, Birgit and Jank, Anne-Marie and
                    Ehgartner, Josef and Nietzsche, Sandor and Dinger, Julia
                    and Kiehntopf, Michael and Funke, Harald and Peters,
                    Frank T. and Lupp, Amelie and Gärtner, Claudia and Mayr,
                    Torsten and Bauer, Michael and Huber, Otmar and Mosig,
                    Alexander S.},
  Title           = {A microfluidically perfused three dimensional human
                    liver model},
  JournalTitle    = {Biomaterials},
  Date            = {2015},
  DOI             = {10.1016/j.biomaterials.2015.08.043},
  Keywords        = {Dynamic cell culture; Liver; Microfluidic biochip;
                    Organoid; Oxygen},
  Pages           = {119--131},
  Volume          = {71}
}

@Article{Repenko:717043,
  Author          = {Repenko, Tatjana and Rix, Anne and Ludwanowski, Simon
                    and Go, Dennis and Kiessling, Fabian and Lederle, Wiltrud
                    and Kuehne, Alexander J. C.},
  Title           = {Bio-degradable highly fluorescent conjugated polymer
                    nanoparticles for bio-medical imaging applications},
  JournalTitle    = {Nat. Commun.},
  Date            = {2017},
  DOI             = {10.1038/s41467-017-00545-0},
  Keywords        = {Lederle-Selection},
  Number          = {1},
  Pages           = {470},
  Volume          = {8}
}

@Article{Reuken2022-zv,
  Author          = {Reuken, Philipp A. and Brozat, Jonathan F. and Quickert,
                    Stefanie and Ibidapo-obe, Oluwatomi and Reißing, Johanna
                    and Franz, Anika and Stengel, Sven and Teichgräber, Ulf
                    K.-M. and Kiehntopf, Michael and Trautwein, Christian and
                    Stallmach, Andreas and Koch, Alexander and Bruns, Tony},
  Title           = {Soluble mannose receptor {CD206} and von Willebrand
                    factor are early biomarkers to identify patients at risk
                    for severe or necrotizing acute pancreatitis},
  JournalTitle    = {J. Intensive Care},
  Date            = {2022},
  DOI             = {10.1186/s40560-022-00619-2},
  Number          = {1},
  Volume          = {10}
}

@Article{Reuken2012-zb,
  Author          = {Reuken, P. A. and Pletz, M. W. and Baier, M. and
                    Pfister, W. and Stallmach, A. and Bruns, T.},
  Title           = {Emergence of spontaneous bacterial peritonitis due to
                    enterococci - risk factors and outcome in a 12-year
                    retrospective study},
  JournalTitle    = {Aliment. Pharmacol. Ther.},
  Date            = {2012},
  DOI             = {10.1111/j.1365-2036.2012.05076.x},
  Keywords        = {Bruns-Selection},
  Number          = {10},
  Pages           = {1199--1208},
  Volume          = {35}
}

@Article{Riba:793498,
  Author          = {Riba, Ambre and Hassani, Kasra and Walker, Alesia and
                    van Best, Niels and von Zeschwitz, Dunja and Anslinger,
                    Teresa and Sillner, Nina and Rosenhain, Stefanie and
                    Eibach, Daniel and Maiga-Ascofaré, Oumou and
                    Rolle-Kampczyk, Ulrike and Basic, Marijana and Binz, Anne
                    and Mocek, Sabine and Sodeik, Beate and Bauerfeind,
                    Rudolf and Mohs, Antje and Trautwein, Christian and
                    Kießling, Fabian and May, Jürgen and Klingenspor,
                    Martin and Gremse, Felix and Schmitt-Kopplin, Philippe
                    and Bleich, André and Torow, Natalia and von Bergen,
                    Martin and Hornef, Mathias W.},
  Title           = {Disturbed gut microbiota and bile homeostasis in
                    Giardia-infected mice contributes to metabolic
                    dysregulation and growth impairment},
  JournalTitle    = {Sci. Transl. Med.},
  Date            = {2020},
  DOI             = {10.1126/scitranslmed.aay7019},
  ids             = {riba2020a},
  Keywords        = {Mohs-Selection,Kießling-Selection,von
                    Bergen-Selection,Hornef-Selection,CRC1382-Project
                    Q01,CRC1382-Project B01,CRC1382-Project
                    Q03,CRC1382-Project Q01,CRC1382-Project
                    Q01,CRC1382-Project A06,CRC1382-Project
                    A08,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {565},
  Pages           = {eaay7019},
  Volume          = {12}
}

@Article{Roderburg2014-pf,
  Author          = {Roderburg, Christoph and Luedde, Tom},
  Title           = {The role of the gut microbiome in the development and
                    progression of liver cirrhosis and hepatocellular
                    carcinoma},
  JournalTitle    = {Gut Microbes},
  Date            = {2014},
  DOI             = {10.4161/gmic.29599},
  Keywords        = {HCC; antibiotics; cirrhosis; gut microbiota; liver},
  Number          = {4},
  Pages           = {441--445},
  Volume          = {5}
}

@Article{Roderburg:195594,
  Author          = {Roderburg, Christoph and Urban, Gerd-Willem and
                    Bettermann, Kira and Vucur, Mihael and Zimmermann,
                    Henning and Schmidt, Sabine and Janssen, Jörn and Koppe,
                    Christiane and Knolle, Percy and Castoldi, Mirco and
                    Tacke, Frank and Trautwein, Christian and Luedde, Tom},
  Title           = {Micro-{RNA} profiling reveals a role for {miR}-29 in
                    human and murine liver fibrosis},
  JournalTitle    = {Hepatology},
  Date            = {2010},
  DOI             = {10.1002/hep.23922},
  Keywords        = {Lüdde-Selection},
  Number          = {1},
  Pages           = {209--218},
  Volume          = {53}
}

@Article{Roderburg:788071,
  Author          = {Roderburg, Christoph and Wree, Alexander and Demir,
                    Münevver and Schmelzle, Moritz and Tacke, Frank},
  Title           = {The role of the innate immune system in the development
                    and treatment of hepatocellular carcinoma},
  JournalTitle    = {Hepatic Oncology},
  Date            = {2020},
  DOI             = {10.2217/hep-2019-0007},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {11 Seiten},
  Volume          = {7}
}

@Article{Rogler2021-eu,
  Author          = {Rogler, Gerhard and Singh, Abha and Kavanaugh, Arthur
                    and Rubin, David T},
  Title           = {Extraintestinal manifestations of inflammatory bowel
                    disease: Current concepts, treatment, and implications
                    for disease management},
  JournalTitle    = {Gastroenterology},
  Date            = {2021},
  DOI             = {10.1053/j.gastro.2021.07.042},
  Keywords        = {Arthralgias; Arthritis; Crohn's Disease; Erythema
                    Nodosum; Extraintestinal Manifestations; Inflammatory
                    Bowel Disease; Primary Sclerosing Cholangitis; Psoriasis;
                    Pyoderma Gangrenosum; Spondyloarthropathy; Ulcerative
                    Colitis; Uveitis},
  Number          = {4},
  Pages           = {1118--1132},
  Volume          = {161}
}

@Article{Roohani:828494,
  Author          = {Roohani, Siyer and Tacke, Frank},
  Title           = {Liver Injury and the Macrophage Issue},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2021},
  DOI             = {10.3390/ijms22147249},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {14},
  Pages           = {7249},
  Subtitle        = {Molecular and Mechanistic Facts and Their Clinical
                    Relevance},
  Volume          = {22}
}

@Article{Rose2021-zh,
  Author          = {Rose, Tracy L. and Weir, William H. and Mayhew, Gregory
                    M. and Shibata, Yoichiro and Eulitt, Patrick and Uronis,
                    Joshua M. and Zhou, Mi and Nielsen, Matthew and Smith,
                    Angela B. and Woods, Michael and Hayward, Michele C. and
                    Salazar, Ashley H. and Milowsky, Matthew I. and Wobker,
                    Sara E. and McGinty, Katrina and Millburn, Michael V. and
                    Eisner, Joel R. and Kim, William Y.},
  Title           = {Fibroblast growth factor receptor 3 alterations and
                    response to immune checkpoint inhibition in metastatic
                    urothelial cancer: {A} real world experience},
  JournalTitle    = {Br. J. Cancer},
  Date            = {2021},
  DOI             = {10.1038/s41416-021-01488-6},
  Number          = {9},
  Pages           = {1251--1260},
  Volume          = {125}
}

@Article{Rosenhain:699837,
  Author          = {Rosenhain, Stefanie and Al Rawashdeh, Wa'el and
                    Kiessling, Fabian and Gremse, Felix},
  Title           = {Sensitivity and accuracy of hybrid fluorescence-mediated
                    tomography in deep tissue regions},
  JournalTitle    = {J. Biophotonics},
  Date            = {2016},
  DOI             = {10.1002/jbio.201600232},
  ids             = {rosenhain2016a},
  Keywords        = {Gremse-Selection},
  Number          = {9},
  Pages           = {1208--1216},
  Volume          = {10}
}

@Article{Rosenhain2018-gc,
  Author          = {Rosenhain, Stefanie and Magnuska, Zuzanna A. and Yamoah,
                    Grace G. and Rawashdeh, Wa’el Al and Kiessling, Fabian
                    and Gremse, Felix},
  Title           = {A preclinical micro-computed tomography database
                    including {3D} whole body organ segmentations},
  JournalTitle    = {Sci. Data},
  Date            = {2018},
  DOI             = {10.1038/sdata.2018.294},
  Number          = {1},
  Pages           = {180294},
  Volume          = {5}
}

@Article{Roy:753990,
  Author          = {Roy, Sanchari and Hooiveld, Guido J. and Seehawer, Marco
                    and Caruso, Stefano and Heinzmann, Florian and Schneider,
                    Anne T. and Frank, Anna K. and Cardenas, David Vargas and
                    Sonntag, Roland and Luedde, Mark and Trautwein, Christian
                    and Stein, Ilan and Pikarsky, Eli and Loosen, Sven and
                    Tacke, Frank and Ringelhan, Marc and Avsaroglu, Seda
                    Kilinc and Goga, Andrei and Buendia, Marie-Annick and
                    Vucur, Mihael and Heikenwalder, Mathias and Zucman-Rossi,
                    Jessica and Zender, Lars and Roderburg, Christoph and
                    Luedde, Tom},
  Title           = {{microRNA} 193a-5p Regulates Levels of Nucleolar- and
                    Spindle-Associated Protein 1 to Suppress
                    Hepatocarcinogenesis},
  JournalTitle    = {Gastroenterology},
  Date            = {2018},
  DOI             = {10.1053/j.gastro.2018.08.032},
  Keywords        = {Lüdde-Selection},
  Number          = {6},
  Pages           = {1951--1966.e26},
  Volume          = {155}
}

@Article{Esterhazy2019-jh,
  Author          = {Esterházy, Daria and Canesso, Maria C. C. and Mesin,
                    Luka and Muller, Paul A. and de Castro, Tiago B. R. and
                    Lockhart, Ainsley and ElJalby, Mahmoud and Faria, Ana M.
                    C. and Mucida, Daniel},
  Title           = {Compartmentalized gut lymph node drainage dictates
                    adaptive immune responses},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-019-1125-3},
  Number          = {7754},
  Pages           = {126--130},
  Volume          = {569}
}

@Article{Rth:698823,
  Author          = {Roeth, Anjali A. and Slabu, Ioana and Baumann, Martin
                    and Alizai, Patrick H. and Schmeding, Maximilian and
                    Guentherodt, Gernot and Schmitz-Rode, Thomas and Neumann,
                    Ulf P.},
  Title           = {Establishment of a biophysical model to optimize
                    endoscopic targeting of magnetic nanoparticles for cancer
                    treatment},
  JournalTitle    = {Int. J. Nanomed.},
  Date            = {2017},
  DOI             = {10.2147/ijn.s132162},
  Keywords        = {Neumann-Selection},
  Pages           = {5933--5940},
  Volume          = {Volume 12}
}

@Article{Rustgi2020-eq,
  Author          = {Rustgi, Sheila D. and Kayal, Maia and Shah, Shailja C.},
  Title           = {Sex-based differences in inflammatory bowel diseases:
                    {A} review},
  JournalTitle    = {Therap. Adv. Gastroenterol.},
  Date            = {2020},
  DOI             = {10.1177/1756284820915043},
  Keywords        = {Crohn's disease; gender; natural history; ulcerative
                    colitis},
  Pages           = {175628482091504},
  Volume          = {13}
}

@Article{Saldanha2022-la,
  Author          = {Saldanha, Oliver Lester and Quirke, Philip and West,
                    Nicholas P. and James, Jacqueline A. and Loughrey,
                    Maurice B. and Grabsch, Heike I. and Salto-Tellez, Manuel
                    and Alwers, Elizabeth and Cifci, Didem and Ghaffari
                    Laleh, Narmin and Seibel, Tobias and Gray, Richard and
                    Hutchins, Gordon G. A. and Brenner, Hermann and van
                    Treeck, Marko and Yuan, Tanwei and Brinker, Titus J. and
                    Chang-Claude, Jenny and Khader, Firas and Schuppert,
                    Andreas and Luedde, Tom and Trautwein, Christian and
                    Muti, Hannah Sophie and Foersch, Sebastian and
                    Hoffmeister, Michael and Truhn, Daniel and Kather, Jakob
                    Nikolas},
  Title           = {Swarm learning for decentralized artificial intelligence
                    in cancer histopathology},
  JournalTitle    = {Nat. Med.},
  Date            = {2022},
  DOI             = {10.1038/s41591-022-01768-5},
  Keywords        = {Trautwein-Selection},
  Number          = {6},
  Pages           = {1232--1239},
  Volume          = {28}
}

@Article{Salem:478849,
  Author          = {Salem, Silvia and Jankowski, Vera and Asare, Yaw and
                    Liehn, Elisa and Welker, Pia and Raya-Bermudez, Ana and
                    Pineda-Martos, Carmen and Rodriguez, Mariano and
                    Muñoz-Castañeda, Juan Rafael and Bruck, Heike and Marx,
                    Nikolaus and Machado, Fernanda B. and Staudt, Mareike and
                    Heinze, Georg and Zidek, Walter and Jankowski, Joachim},
  Title           = {Identification of the Vasoconstriction-Inhibiting Factor
                    {(VIF),} a Potent Endogenous Cofactor of Angiotensin {II}
                    Acting on the Angiotensin {II} Type 2 Receptor},
  JournalTitle    = {Circulation},
  Addendum        = preliminarywork,
  Date            = {2015},
  DOI             = {10.1161/circulationaha.114.013168},
  Keywords        = {Jankowski-Selection},
  Number          = {16},
  Pages           = {1426--1434},
  Volume          = {131}
}

@Article{Schaap2004,
  Author          = {Schaap, Frank G. and Rensen, Patrick C.N. and Voshol,
                    Peter J. and Vrins, Carlos and van der Vliet, Hendrik N.
                    and Chamuleau, Robert A.F.M. and Havekes, Louis M. and
                    Groen, Albert K. and van Dijk, Ko Willems},
  Title           = {{ApoAV} Reduces Plasma Triglycerides by Inhibiting Very
                    Low Density Lipoprotein-Triglyceride {(VLDL}-{TG)}
                    Production and Stimulating Lipoprotein Lipase-mediated
                    {VLDL}-{TG} Hydrolysis},
  JournalTitle    = {J. Biol. Chem.},
  Date            = {2004},
  DOI             = {10.1074/jbc.m403240200},
  Number          = {27},
  Pages           = {27941--27947},
  Volume          = {279}
}

@Article{Schaap2008,
  Author          = {Schaap, Frank G. and van der Gaag, Niels A. and Gouma,
                    Dirk J. and Jansen, Peter L. M.},
  Title           = {High expression of the bile salt-homeostatic hormone
                    fibroblast growth factor 19 in the liver of patients with
                    extrahepatic cholestasis},
  JournalTitle    = {Hepatology},
  Date            = {2008},
  DOI             = {10.1002/hep.22771},
  Keywords        = {Schaap-Selection},
  Number          = {4},
  Pages           = {1228--1235},
  Volume          = {49}
}

@Article{Schaap2013,
  Author          = {Schaap, Frank G. and Leclercq, Isabelle A. and Jansen,
                    Peter L.M. and Olde Damink, Steven W.},
  Title           = {Prometheus’ little helper, a novel role for fibroblast
                    growth factor 15 in compensatory liver growth},
  JournalTitle    = {J. Hepatol.},
  Date            = {2013},
  DOI             = {10.1016/j.jhep.2013.07.013},
  Number          = {5},
  Pages           = {1121--1123},
  Volume          = {59}
}

@Article{Schaap2013a,
  Author          = {Schaap, Frank G. and Trauner, Michael and Jansen, Peter
                    L. M.},
  Title           = {Bile acid receptors as targets for drug development},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2013},
  DOI             = {10.1038/nrgastro.2013.151},
  Keywords        = {Schaap-Selection},
  Number          = {1},
  Pages           = {55--67},
  Volume          = {11}
}

@Article{Schaap2014,
  Author          = {Schaap, Frank G. and Jansen, Peter L.M. and Olde Damink,
                    Steven W.M.},
  Title           = {{FXR,} intestinal {FiXeR} of hepatocellular carcinoma?},
  JournalTitle    = {Hepatology},
  Date            = {2014},
  DOI             = {10.1002/hep.27397},
  Keywords        = {Olde Damink-Selection},
  Number          = {1},
  Pages           = {21--23},
  Volume          = {61}
}

@Article{Schaap:718185,
  Author          = {Schaap, Frank G. and Jansen, Peter L.M. and Olde Damink,
                    Steven W.M.},
  Title           = {Chronic elevation of plasma fibroblast growth factor 19
                    in long‐term farnesoid X receptor agonist therapy, a
                    happy marriage or cause for oncological concern?},
  JournalTitle    = {Hepatology},
  Date            = {2017},
  DOI             = {10.1002/hep.29511},
  Number          = {2},
  Pages           = {782--784},
  Volume          = {67}
}

@Patent{SchaapDamink-patent1,
  Title           = {Methods of promoting hepatic regeneration},
  Number          = {US Patent Application No. 15/760,769}
}

@Patent{Morath2022-patent,
  Author          = {Morath, V. and Skerra, W. and Fritschle, A.},
  Title           = {Patent no. WO2022101492: Bioorthogonal reporter gene
                    system.73., 2022},
  Date            = {2022}
}

@Article{Schaubeck2015,
  Author          = {Schaubeck, Monika and Clavel, Thomas and Calasan, Jelena
                    and Lagkouvardos, Ilias and Haange, Sven Bastiaan and
                    Jehmlich, Nico and Basic, Marijana and Dupont, Aline and
                    Hornef, Mathias and Bergen, Martin von and Bleich, André
                    and Haller, Dirk},
  Title           = {Dysbiotic gut microbiota causes transmissible Crohn's
                    disease-like ileitis independent of failure in
                    antimicrobial defence},
  JournalTitle    = {Gut},
  Date            = {2015},
  DOI             = {10.1136/gutjnl-2015-309333},
  ids             = {schaubeck2016a},
  Keywords        = {von Bergen-Selection},
  Number          = {2},
  Pages           = {225--237},
  Volume          = {65}
}

@Article{Dycaico1988-ix,
  Author          = {Dycaico, Mark J. and Grant, Seth G. N. and Felts,
                    Katherine and Nichols, W. Stephen and Geller, Stephen A.
                    and Hager, Jeffrey H. and Pollard, Amy J. and Kohler,
                    Steven W. and Short, Heidi P. and Jirik, Frank R. and
                    Hanahan, Douglas and Sorge, Joseph A.},
  Title           = {Neonatal Hepatitis Induced by α\textsubscript{1}
                    -Antitrypsin: {A} Transgenic Mouse Model},
  JournalTitle    = {Science},
  Date            = {1988},
  DOI             = {10.1126/science.3264419},
  Number          = {4884},
  Pages           = {1409--1412},
  Volume          = {242}
}

@Article{Schierwagen2015-ez,
  Author          = {Schierwagen, Robert and Maybüchen, Lara and Zimmer,
                    Sebastian and Hittatiya, Kanishka and Bäck, Christer and
                    Klein, Sabine and Uschner, Frank E and Reul, Winfried and
                    Boor, Peter and Nickenig, Georg and Strassburg, Christian
                    P and Trautwein, Christian and Plat, Jogchum and
                    Lütjohann, Dieter and Sauerbruch, Tilman and Tacke,
                    Frank and Trebicka, Jonel},
  Title           = {Seven weeks of Western diet in
                    apolipoprotein-E-deficient mice induce metabolic syndrome
                    and non-alcoholic steatohepatitis with liver fibrosis},
  JournalTitle    = {Sci. Rep.},
  Date            = {2015},
  DOI             = {10.1038/srep12931},
  Number          = {1},
  Pages           = {12931},
  Volume          = {5}
}

@Article{Tyc2020,
  Author          = {Tyc, Olaf and Jansen, Christian and Schierwagen, Robert
                    and Uschner, Frank Erhard and Israelsen, Mads and Klein,
                    Sabine and Ortiz, Cristina and Strassburg, Christian P.
                    and Zeuzem, Stefan and Gu, Wenyi and Torres, Sandra and
                    Praktiknjo, Michael and Kersting, Stephan and
                    Langheinrich, Melanie and Nattermann, Jacob and Servant,
                    Florence and Arumugam, Manimozhiyan and Krag, Aleksander
                    and Lelouvier, Benjamin and Weismüller, Tobias J. and
                    Trebicka, Jonel},
  DOI             = {10.1002/lt.25882},
  Year            = {2020},
  Volume          = {26},
  Number          = {12},
  Pages           = {1652--1657},
  Title           = {Variation in Bile Microbiome by the Etiology of
                    Cholestatic Liver Disease},
  JournalTitle    = {Liver Transplant.},
  Keywords = {Trebicka-Selection},
}


@Article{Schierwagen2018,
  Author          = {Schierwagen, Robert and Alvarez-Silva, Camila and
                    Madsen, Mette Simone Aae and Kolbe, Carl Christian and
                    Meyer, Carsten and Thomas, Daniel and Uschner, Frank
                    Erhard and Magdaleno, Fernando and Jansen, Christian and
                    Pohlmann, Alessandra and Praktiknjo, Michael and
                    Hischebeth, Gunnar T and Molitor, Ernst and Latz, Eicke
                    and Lelouvier, Benjamin and Trebicka, Jonel and Arumugam,
                    Manimozhiyan},
  Title           = {Circulating microbiome in blood of different circulatory
                    compartments},
  JournalTitle    = {Gut},
  Date            = {2018},
  author+an:default = {16=equal;17=equal},
  Addendum        = equal,
  DOI             = {10.1136/gutjnl-2018-316227},
  ids             = {schierwagen_circulating_2019},
  Number          = {3},
  Pages           = {578--580},
  Volume          = {68}
}

@Article{Schierwagen2020-hd,
  Author          = {Schierwagen, Robert and Alvarez-Silva, Camila and
                    Servant, Florence and Trebicka, Jonel and Lelouvier,
                    Benjamin and Arumugam, Manimozhiyan},
  Title           = {Trust is good, control is better: technical
                    considerations in blood microbiome analysis},
  JournalTitle    = {Gut},
  Date            = {2020},
  DOI             = {10.1136/gutjnl-2019-319123},
  Keywords        = {bacterial infection; intestinal microbiology},
  Number          = {7},
  Pages           = {1362--1363},
  Volume          = {69}
}

@Article{Schierwagen:815762,
  Author          = {Schierwagen, Robert and Uschner, Frank E. and Ortiz,
                    Cristina and Torres, Sandra and Brol, Max J. and Tyc,
                    Olaf and Gu, Wenyi and Grimm, Christian and Zeuzem,
                    Stefan and Plamper, Andreas and Pfeifer, Philipp and
                    Zimmer, Sebastian and Welsch, Christoph and Schaefer,
                    Liliana and Rheinwalt, Karl P. and Clària, Joan and
                    Arroyo, Vicente and Trebicka, Jonel and Klein, Sabine},
  Title           = {The Role of Macrophage-Inducible C-Type Lectin in
                    Different Stages of Chronic Liver Disease},
  JournalTitle    = {Front. Immunol.},
  Date            = {2020},
  DOI             = {10.3389/fimmu.2020.01352},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project A09,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {1352},
  Volume          = {11}
}

@Article{Schierwagen:834280,
  Author          = {Schierwagen, Robert and Dietrich, Peter and Klein,
                    Sabine and Uschner, Frank Erhard and Ortiz, Cristina and
                    Tyc, Olaf and Torres, Sandra and Hellerbrand, Claus and
                    Sauerbruch, Tilman and Trebicka, Jonel},
  Title           = {β-Arrestin2 is increased in liver fibrosis in humans
                    and rodents},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2020},
  DOI             = {10.1073/pnas.2014337117},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project A09,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {44},
  Pages           = {27082--27084},
  Volume          = {117}
}

@Article{Schippers:133974,
  Author          = {Schippers, Angela and Leuker, Christoph and Pabst,
                    Oliver and Kochut, Annika and Prochnow, Blair and Gruber,
                    Achim D. and Leung, Euphemia and Krissansen, Geoffrey W.
                    and Wagner, Norbert and Müller, Werner},
  Title           = {Mucosal Addressin Cell-Adhesion Molecule-1 Controls
                    Plasma-Cell Migration and Function in the Small Intestine
                    of Mice},
  JournalTitle    = {Gastroenterology},
  Date            = {2009},
  Addendum        = sharedlast,
  author+an:default = {10=sharedLast;9=sharedLast},
  DOI             = {10.1053/j.gastro.2009.05.039},
  Keywords        = {Schippers-Selection,Wagner-Selection},
  Number          = {3},
  Pages           = {924--933},
  Volume          = {137}
}

@Article{Schippers:164493,
  Author          = {Schippers, Angela and Mateika, Silke and Prochnow, Blair
                    and Gruber, Achim D. and Müller, Werner and Frischmann,
                    Ursula},
  Title           = {Susceptibility of four inbred mouse strains to a
                    low-pathogenic isolate of Yersinia enterocolitica},
  JournalTitle    = {Mamm. Genome},
  Date            = {2008},
  DOI             = {10.1007/s00335-008-9105-1},
  Number          = {4},
  Pages           = {279--291},
  Volume          = {19}
}

@Article{Schippers:196538,
  Author          = {Schippers, Angela and Kochut, Annika and Pabst, Oliver
                    and Frischmann, Ursula and Clahsen, Thomas and Tenbrock,
                    Klaus and Müller, Werner and Wagner, Norbert},
  Title           = {β7 integrin controls immunogenic and tolerogenic
                    mucosal B cell responses},
  JournalTitle    = {Clin. Immunol.},
  Date            = {2012},
  DOI             = {10.1016/j.clim.2012.05.008},
  Keywords        = {Schippers-Selection},
  Number          = {2},
  Pages           = {87--97},
  Volume          = {144}
}

@Article{Schippers:570353,
  Author          = {Schippers, Angela and Muschaweck, M and Clahsen, T and
                    Tautorat, S and Grieb, L and Tenbrock, K and Gaßler, N
                    and Wagner, Norbert},
  Title           = {β7-Integrin exacerbates experimental {DSS}-induced
                    colitis in mice by directing inflammatory monocytes into
                    the colon},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2016},
  DOI             = {10.1038/mi.2015.82},
  ids             = {Schippers2016a},
  Keywords        = {Schippers-Selection,Wagner-Selection},
  Number          = {2},
  Pages           = {527--538},
  Volume          = {9}
}

@Article{Schippers:808794,
  Author          = {Schippers, Angela and Hübel, Jessica and Heymann, Felix
                    and Clahsen, Thomas and Eswaran, Sreepradha and
                    Schlepütz, Sarah and Püllen, Robin and Gaßler,
                    Nikolaus and Tenbrock, Klaus and Tacke, Frank and Wagner,
                    Norbert},
  Title           = {{MA}d{CAM}-1/α4β7 Integrin-Mediated
                    Lymphocyte/Endothelium Interactions Exacerbate Acute
                    Immune-Mediated Hepatitis in Mice},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jcmgh.2020.12.003},
  ids             = {Schippers2021-ih},
  Keywords        = {Schippers-Selection,Wagner-Selection,CRC1382-Project
                    B02,CRC1382-Project B02,CRC1382-Project
                    B05,CRC1382-Project B02},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {1227--1250.el},
  ShortJournal    = {CMGH},
  Volume          = {11}
}

@Article{Schmid2010,
  Author          = {Schmid, Andreas and Blank, Lars M.},
  Title           = {Hypothesis-driven omics integration},
  JournalTitle    = {Nat. Chem. Biol.},
  Date            = {2010},
  DOI             = {10.1038/nchembio.398},
  Number          = {7},
  Pages           = {485--487},
  Volume          = {6}
}

@Article{Schmitz:753909,
  Author          = {Schmitz, Corinna and Noels, Heidi and Bounkari, Omar El
                    and Straussfeld, Eva and Megens, Remco T. A. and
                    Sternkopf, Marieke and Alampour‐Rajabi, Setareh and
                    Krammer, Christine and Tilstam, Pathricia V. and Gerdes,
                    Norbert and Bürger, Christina and Kapurniotu, Aphrodite
                    and Bucala, Richard and Jankowski, Joachim and Weber,
                    Christian and Bernhagen, Jürgen},
  Title           = {Mif-deficiency favors an atheroprotective autoantibody
                    phenotype in atherosclerosis},
  Addendum        = equal,
  JournalTitle    = {The FASEB Journal},
  Date            = {2018},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1096/fj.201800058r},
  Keywords        = {Noels-Selection},
  Number          = {8},
  Pages           = {4428--4443},
  Volume          = {32}
}

@Article{Vergani2022-hg,
  Author          = {Vergani, Stefano and Muleta, Konjit Getachew and Da
                    Silva, Clément and Doyle, Alexander and Kristiansen,
                    Trine Ahn and Sodini, Selene and Krausse, Niklas and
                    Montano, Giorgia and Kotarsky, Knut and Nakawesi, Joy and
                    Åkerstrand, Hugo and Vanhee, Stijn and Gupta, Sneh Lata
                    and Bryder, David and Agace, William Winston and Lahl,
                    Katharina and Yuan, Joan},
  Title           = {A self-sustaining layer of early-life-origin B cells
                    drives steady-state {IgA} responses in the adult gut},
  JournalTitle    = {Immunity},
  Date            = {2022},
  DOI             = {10.1016/j.immuni.2022.08.018},
  Number          = {10},
  Pages           = {1829--1842.e6},
  Volume          = {55}
}

@Article{Wollenhaupt2022-wf,
  Author          = {Wollenhaupt, Julia and Frisch, Janina and Harlacher, Eva
                    and Wong, Dickson W.L. and Jin, Han and Schulte, Corinna
                    and Vondenhoff, Sonja and Moellmann, Julia and
                    Klinkhammer, Barbara Mara and Zhang, Li and
                    Baleanu-Curaj, Adelina and Liehn, Elisa A. and Speer,
                    Thimoteus and Kazakov, Andrey and Werner, Christian and
                    van der Vorst, Emiel P.C. and Selejan, Simina-Ramona and
                    Hohl, Mathias and Böhm, Michael and Kramann, Rafael and
                    Biessen, Erik A.L. and Lehrke, Michael and Marx, Nikolaus
                    and Jankowski, Joachim and Maack, Christoph and Boor,
                    Peter and Prates Roma, Leticia and Noels, Heidi},
  Title           = {Pro-oxidative priming but maintained cardiac function in
                    a broad spectrum of murine models of chronic kidney
                    disease},
  JournalTitle    = {Redox Biol.},
  Date            = {2022},
  DOI             = {10.1016/j.redox.2022.102459},
  Keywords        = {Noels-Selection},
  Number          = {102459},
  Pages           = {102459},
  Volume          = {56}
}

@Article{Schneider2019-yw,
  Author          = {Schneider, Kai Markus and Mohs, Antje and Kilic, Konrad
                    and Candels, Lena Susanna and Elfers, Carsten and Bennek,
                    Eveline and Schneider, Lukas Ben and Heymann, Felix and
                    Gassler, Nikolaus and Penders, John and Trautwein,
                    Christian},
  Title           = {Intestinal Microbiota protects against {MCD}
                    diet-induced steatohepatitis},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2019},
  DOI             = {10.3390/ijms20020308},
  Keywords        = {Candels-Selection,SchneiderKM-Selection},
  Number          = {2},
  Volume          = {20}
}

@Article{Schneider2021-fq,
  Author          = {Schneider, Kai Markus and Candels, Lena Susanna and Hov,
                    Johannes R and Myllys, Maiju and Hassan, Reham and
                    Schneider, Carolin Victoria and Wahlström, Annika and
                    Mohs, Antje and Zühlke, Sebastian and Liao, Lijun and
                    Elfers, Carsten and Kilic, Konrad and Henricsson, Marcus
                    and Molinaro, Antonio and Hatting, Maximilian and Zaza,
                    Ayham and Drasdo, Dirk and Frissen, Mick and Devlin, A
                    Sloan and Gálvez, Eric J C and Strowig, Till and
                    Karlsen, Tom H and Hengstler, Jan G and Marschall,
                    Hanns-Ulrich and Ghallab, Ahmed and Trautwein,
                    Christian},
  Title           = {Gut microbiota depletion exacerbates cholestatic liver
                    injury via loss of {FXR} signalling},
  JournalTitle    = {Nat. Metab.},
  Date            = {2021},
  author+an:default = {1=equal;2=equal},
  Addendum        = equalpreliminarywork,
  DOI             = {10.1038/s42255-021-00452-1},
  Keywords        = {Candels-Selection,SchneiderKM-Selection,Mohs-Selection,Trautwein-Selection},
  Number          = {9},
  Pages           = {1228--1241},
  Volume          = {3}
}

@Article{Schneider2022-cc,
  Author          = {Schneider, Carolin V. and Schneider, Kai Markus and
                    Teumer, Alexander and Rudolph, Karl Lenhard and Hartmann,
                    Daniel and Rader, Daniel J. and Strnad, Pavel},
  Title           = {Association of Telomere Length With Risk of Disease and
                    Mortality},
  JournalTitle    = {JAMA Intern. Med.},
  Date            = {2022},
  DOI             = {10.1001/jamainternmed.2021.7804},
  Keywords        = {SchneiderCV-Selection,Strnad-Selection},
  Number          = {3},
  Pages           = {291},
  Volume          = {182}
}

@Article{Schneider2022-mg,
  Author          = {Schneider, Carolin V. and Schneider, Kai Markus},
  Title           = {New equations for estimating the {GFR} without race},
  JournalTitle    = {N. Engl. J. Med.},
  Date            = {2022},
  DOI             = {10.1056/NEJMc2119761},
  Keywords        = {SchneiderKM-Selection},
  Number          = {17},
  Pages           = {1671--1672},
  Volume          = {386}
}

@Article{Schneider2022-se,
  Author          = {Schneider, Annika R P and Schneider, Carolin V. and
                    Schneider, Kai Markus and Baier, Vanessa and Schaper,
                    Steffen and Diedrich, Christian and Coboeken, Katrin and
                    Mayer, Hannah and Gu, Wenyi and Trebicka, Jonel and
                    Blank, Lars M. and Burghaus, Rolf and Lippert, Joerg and
                    Rader, Daniel J and Thaiss, Christoph A and Schlender,
                    Jan-Frederik and Trautwein, Christian and Kuepfer, Lars},
  Title           = {Early prediction of decompensation ({EPOD}) score:
                    Non-invasive determination of cirrhosis decompensation
                    risk},
  JournalTitle    = {Liver Int.},
  Date            = {2022},
  DOI             = {10.1111/liv.15161},
  ids             = {Schneider2022-xb},
  Keywords        = {Küpfer-Selection},
  Number          = {3},
  Pages           = {640--650},
  Volume          = {42}
}

@Article{Schneider:685016,
  Author          = {Schneider, Anne T. and Gautheron, Jérémie and Tacke,
                    Frank and Vucur, Mihael and Luedde, Tom},
  Title           = {Receptor interacting protein kinase 1 {(RIPK1)} in
                    hepatocytes does not mediate murine acetaminophen
                    toxicity},
  JournalTitle    = {Hepatology},
  Date            = {2015},
  DOI             = {10.1002/hep.28225},
  Keywords        = {Lüdde-Selection},
  Number          = {1},
  Pages           = {306--308},
  Volume          = {64}
}

@Article{Schneider:719057,
  Author          = {Schneider, A.T. and Gautheron, J. and Feoktistova, M.
                    and Roderburg, C. and Loosen, S.H. and Schemmer, P. and
                    Büchler, M.W. and Neumann, U.P. and Tacke, F. and
                    Trautwein, C. and Longerich, T. and Vucur, M. and Luedde,
                    T.},
  Title           = {{RIPK1} suppresses a {TRAF2}-dependent pathway to liver
                    cancer},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/s0168-8278(17)30759-6},
  Keywords        = {Lüdde-Selection,Neumann-Selection},
  Number          = {1},
  Organization    = {The International Liver Congress TM 2017 — 52nd Annual
                    meeting of the European Association for the Study of the
                    Liver, Amsterdam (Netherlands), 19 Apr 2017 - 23 Apr
                    2017},
  Pages           = {S229},
  Volume          = {66}
}

@Article{Schneider:808392,
  Author          = {Schneider, Carolin Victoria and Kleinjans, Moritz and
                    Fromme, Malin and Schneider, Kai Markus and Strnad,
                    Pavel},
  Title           = {Phenome-wide association study in adult coeliac
                    disease},
  JournalTitle    = {Aliment. Pharmacol. Ther.},
  Date            = {2021},
  DOI             = {10.1111/apt.16206},
  Keywords        = {SchneiderCV-Selection,CRC1382-Project A03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {510--518},
  Subtitle        = {Role of {HLA} subtype},
  Volume          = {53}
}

@Article{Kolodziejczyk2019,
  Author          = {Kolodziejczyk, Aleksandra A. and Zheng, Danping and
                    Elinav, Eran},
  Title           = {Diet–microbiota interactions and personalized
                    nutrition},
  JournalTitle    = {Nat. Rev. Microbiol.},
  Date            = {2019},
  DOI             = {10.1038/s41579-019-0256-8},
  Number          = {12},
  Pages           = {742--753},
  Volume          = {17}
}

@Article{Schneider:815759,
  Author          = {Schneider, Kai Markus and Elfers, Carsten and Ghallab,
                    Ahmed and Schneider, Carolin Victoria and Galvez, Eric J.
                    C. and Mohs, Antje and Gui, Wenfang and Candels, Lena
                    Susanna and Wirtz, Theresa H. and Zuehlke, Sebastian and
                    Spiteller, Michael and Myllys, Maiju and Roulet, Alain
                    and Ouzerdine, Amirouche and Lelouvier, Benjamin and
                    Kilic, Konrad and Liao, Lijun and Nier, Anika and Latz,
                    Eicke and Bergheim, Ina and Thaiss, Christoph A. and
                    Hengstler, Jan G. and Strowig, Till and Trautwein,
                    Christian},
  Title           = {Intestinal Dysbiosis Amplifies Acetaminophen-Induced
                    Acute Liver Injury},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2021},
  author+an:default = {1=equal;2=equal},
  Addendum        = equal,
  DOI             = {10.1016/j.jcmgh.2020.11.002},
  ids             = {Schneider2021Intestinal,Schneider2021-or},
  Keywords        = {Wirtz-Selection,Candels-Selection,SchneiderKM-Selection,Trautwein-Selection,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {909--933},
  ShortJournal    = {CMGH},
  Volume          = {11}
}

@Article{SchneiderCV-extra,
  Author          = {Schneider, Carolin and Strnad, Pavel},
  Title           = {Case 3: How would you manage this 58-year-old, Pi*ZZ
                    genotype woman with recurrently elevated liver enzymes?},
  JournalTitle    = {ERS Monograph},
  Date            = {2019},
  Keywords        = {SchneiderCV-Selection}
}

@Article{Schober:231944,
  Author          = {Schober, Andreas and Nazari-Jahantigh, Maliheh and Wei,
                    Yuanyuan and Bidzhekov, Kiril and Gremse, Felix and
                    Grommes, Jochen and Megens, Remco T A and Heyll, Kathrin
                    and Noels, Heidi and Hristov, Michael and Wang, Shusheng
                    and Kiessling, Fabian and Olson, Eric N and Weber,
                    Christian},
  Title           = {{MicroRNA}-126-5p promotes endothelial proliferation and
                    limits atherosclerosis by suppressing Dlk1},
  JournalTitle    = {Nat. Med.},
  Date            = {2014},
  DOI             = {10.1038/nm.3487},
  Keywords        = {Gremse-Selection},
  Number          = {4},
  Pages           = {368--376},
  Volume          = {20}
}

@Article{Schoultz2020-xi,
  Author          = {Schoultz, Ida and Keita, {Å}sa V},
  Title           = {The intestinal barrier and current techniques for the
                    assessment of gut permeability},
  JournalTitle    = {Cells},
  Date            = {2020},
  DOI             = {10.3390/cells9081909},
  Number          = {8},
  Pages           = {1909},
  Volume          = {9}
}

@Article{Schreder:569507,
  Author          = {Schreder, Alina and Moschovakis, Georgios Leandros and
                    Halle, Stephan and Schlue, Jerome and Lee, Chun-Wei and
                    Schippers, Angela and David, Sascha and Bernhardt,
                    Günter and Ganser, Arnold and Pabst, Oliver and
                    Förster, Reinhold and Koenecke, Christian},
  Title           = {Differential Effects of Gut-Homing Molecules {CC}
                    Chemokine Receptor 9 and Integrin-β7 during Acute
                    Graft-versus-Host Disease of the Liver},
  JournalTitle    = {Biol. Blood Marrow Tr.},
  Date            = {2015},
  DOI             = {10.1016/j.bbmt.2015.08.038},
  Number          = {12},
  Pages           = {2069--2078},
  Volume          = {21}
}

@Article{Schreuder2010,
  Author          = {Schreuder, Tim C. M. A. and Marsman, Hendrik A. and
                    Lenicek, Martin and van Werven, Jochem R. and Nederveen,
                    Aart J. and Jansen, Peter L. M. and Schaap, Frank G.},
  Title           = {The hepatic response to {FGF19} is impaired in patients
                    with nonalcoholic fatty liver disease and insulin
                    resistance},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2010},
  DOI             = {10.1152/ajpgi.00322.2009},
  Number          = {3},
  Pages           = {G440--G445},
  Volume          = {298}
}

@Article{Schubert:699712,
  Author          = {Schubert, Kristin and Olde Damink, Steven W. M. and von
                    Bergen, Martin and Schaap, Frank G.},
  Title           = {Interactions between bile salts, gut microbiota, and
                    hepatic innate immunity},
  JournalTitle    = {Immunol. Rev.},
  Date            = {2017},
  DOI             = {10.1111/imr.12579},
  ids             = {schubert2017a},
  Keywords        = {Schaap-Selection,von Bergen-Selection},
  Number          = {1},
  Pages           = {23--35},
  Volume          = {279}
}

@Article{Schubert:848653,
  Author          = {Schubert, Kristin and Karkossa, Isabel and Schor, Jana
                    and Engelmann, Beatrice and Steinheuer, Lisa Maria and
                    Bruns, Tony and Rolle-Kampczyk, Ulrike and Hackermüller,
                    Jörg and von Bergen, Martin},
  Title           = {A multi-omics analysis of mucosal-associated-invariant
                    {T} cells reveals key drivers of distinct modes of
                    activation},
  JournalTitle    = {Front. Immunol.},
  Date            = {2021},
  DOI             = {10.3389/fimmu.2021.616967},
  ids             = {Schubert2021-en},
  Keywords        = {MAIT cells; TCR-dependent; TCR-independent; activation;
                    key driver analysis; multi-omics analysis},
  Pages           = {616967},
  Volume          = {12}
}

@Article{Bajaj2012-ye,
  Author          = {Bajaj, Jasmohan S. and Hylemon, Phillip B. and Ridlon,
                    Jason M. and Heuman, Douglas M. and Daita, Kalyani and
                    White, Melanie B. and Monteith, Pamela and Noble, Nicole
                    A. and Sikaroodi, Masoumeh and Gillevet, Patrick M.},
  Title           = {Colonic mucosal microbiome differs from stool microbiome
                    in cirrhosis and hepatic encephalopathy and is linked to
                    cognition and inflammation},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2012},
  DOI             = {10.1152/ajpgi.00152.2012},
  Number          = {6},
  Pages           = {G675--G685},
  Volume          = {303}
}

@Article{Schulz:464885,
  Author          = {Schulz, O. and Ugur, M and Friedrichsen, M and
                    Radulovic, K and Niess, J-H and Jalkanen, S and Krueger,
                    A and Pabst, Oliver},
  Title           = {Hypertrophy of infected Peyer’s patches arises from
                    global, interferon-receptor, and {CD69}-independent
                    shutdown of lymphocyte egress},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2013},
  DOI             = {10.1038/mi.2013.105},
  Keywords        = {Pabst-Selection},
  Number          = {4},
  Pages           = {892--904},
  Volume          = {7}
}

@Article{Schulz:789319,
  Author          = {Schulz, Olga and Jaensson, Elin and Persson, Emma K. and
                    Liu, Xiaosun and Worbs, Tim and Agace, William W. and
                    Pabst, Oliver},
  Title           = {Intestinal {CD103+,} but not {CX3CR1+,} antigen sampling
                    cells migrate in lymph and serve classical dendritic cell
                    functions},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2009},
  DOI             = {10.1084/jem.20091925},
  Number          = {13},
  Pages           = {3101--3114},
  ShortJournal    = {JEM},
  Volume          = {206}
}

@Article{Schwarzkopf:834281,
  Author          = {Schwarzkopf, Katharina Maria and Eberle, Larissa and
                    Uschner, Frank Erhard and Klein, Sabine and Schierwagen,
                    Robert and Mücke, Marcus Maximilian and Schaefer,
                    Liliana and Clària, Joan and Zeuzem, Stefan and
                    Hintermann, Edith and Christen, Urs and Lange, Christian
                    Markus and Trebicka, Jonel and Welsch, Christoph},
  Title           = {Interleukin-22 in acute-on-chronic liver failure: A
                    matter of ineffective levels, receptor dysregulation or
                    defective signalling?},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jhep.2020.05.012},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {4},
  Pages           = {980--982},
  Volume          = {73}
}

@Article{Schwimmer2019Microbiome,
  Author          = {Schwimmer, Jeffrey B. and Johnson, Jethro S. and
                    Angeles, Jorge E. and Behling, Cynthia and Belt, Patricia
                    H. and Borecki, Ingrid and Bross, Craig and Durelle,
                    Janis and Goyal, Nidhi P. and Hamilton, Gavin and Holtz,
                    Mary L. and Lavine, Joel E. and Mitreva, Makedonka and
                    Newton, Kimberly P. and Pan, Amy and Simpson, Pippa M.
                    and Sirlin, Claude B. and Sodergren, Erica and Tyagi,
                    Rahul and Yates, Katherine P. and Weinstock, George M.
                    and Salzman, Nita H.},
  Title           = {Microbiome Signatures Associated With Steatohepatitis
                    and Moderate to Severe Fibrosis in Children With
                    Nonalcoholic Fatty Liver Disease},
  JournalTitle    = {Gastroenterology},
  Date            = {2019-10},
  DOI             = {10.1053/j.gastro.2019.06.028},
  Number          = {4},
  Pages           = {1109--1122},
  Volume          = {157}
}

@Article{Schwinge2017-yb,
  Author          = {Schwinge, Dorothee and von Haxthausen, Franziska and
                    Quaas, Alexander and Carambia, Antonella and Otto,
                    Benjamin and Glaser, Fabian and Höh, Benedikt and
                    Thiele, Nina and Schoknecht, Tanja and Huber, Samuel and
                    Steffens, Niklas and Lohse, Ansgar W. and Herkel,
                    Johannes and Schramm, Christoph},
  Title           = {Dysfunction of hepatic regulatory T cells in
                    experimental sclerosing cholangitis is related to {IL}-12
                    signaling},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/j.jhep.2016.12.001},
  Keywords        = {IL-12 receptor; IL-2/IL-2Ab complex; Primary sclerosing
                    cholangitis; Treg expansion},
  Number          = {4},
  Pages           = {798--805},
  Volume          = {66}
}

@Article{Seeley2018,
  Author          = {Seeley, John J. and Baker, Rebecca G. and Mohamed, Ghait
                    and Bruns, Tony and Hayden, Matthew S. and Deshmukh,
                    Sachin D. and Freedberg, Daniel E. and Ghosh, Sankar},
  Title           = {Induction of innate immune memory via {microRNA}
                    targeting of chromatin remodelling factors},
  JournalTitle    = {Nature},
  Date            = {2018},
  DOI             = {10.1038/s41586-018-0253-5},
  Keywords        = {Bruns-Selection},
  Number          = {7712},
  Pages           = {114--119},
  Volume          = {559}
}

@Article{Li2021-it,
  Author          = {Li, Zhijian and Kuppe, Christoph and Ziegler, Susanne
                    and Cheng, Mingbo and Kabgani, Nazanin and Menzel, Sylvia
                    and Zenke, Martin and Kramann, Rafael and Costa, Ivan
                    G.},
  Title           = {Chromatin-accessibility estimation from single-cell
                    {ATAC}-seq data with {scOpen}},
  JournalTitle    = {Nat. Commun.},
  Date            = {2021},
  DOI             = {10.1038/s41467-021-26530-2},
  Number          = {1},
  Pages           = {6386},
  Volume          = {12}
}

@Article{Seidman2020-ye,
  Author          = {Seidman, Jason S. and Troutman, Ty D. and Sakai, Mashito
                    and Gola, Anita and Spann, Nathanael J. and Bennett,
                    Hunter and Bruni, Cassi M. and Ouyang, Zhengyu and Li,
                    Rick Z. and Sun, Xiaoli and Vu, BaoChau T. and Pasillas,
                    Martina P. and Ego, Kaori M. and Gosselin, David and
                    Link, Verena M. and Chong, Ling-Wa and Evans, Ronald M.
                    and Thompson, Bonne M. and McDonald, Jeffrey G. and
                    Hosseini, Mojgan and Witztum, Joseph L. and Germain,
                    Ronald N. and Glass, Christopher K.},
  Title           = {Niche-Specific Reprogramming of Epigenetic Landscapes
                    Drives Myeloid Cell Diversity in Nonalcoholic
                    Steatohepatitis},
  JournalTitle    = {Immunity},
  Date            = {2020},
  DOI             = {10.1016/j.immuni.2020.04.001},
  Number          = {6},
  Pages           = {1057--1074.e7},
  Volume          = {52}
}

@Article{Seifert2012,
  Author          = {Seifert, Jana and Taubert, Martin and Jehmlich, Nico and
                    Schmidt, Frank and Völker, Uwe and Vogt, Carsten and
                    Richnow, Hans-Hermann and von Bergen, Martin},
  Title           = {Protein-based stable isotope probing (protein-{SIP)} in
                    functional metaproteomics},
  JournalTitle    = {Mass Spectrom. Rev.},
  Date            = {2012},
  DOI             = {10.1002/mas.21346},
  Number          = {6},
  Pages           = {683--697},
  Subtitle        = {PROTEIN-BASED STABLE ISOTOPE PROBING},
  Volume          = {31}
}

@Article{Seikrit:824679,
  Author          = {Seikrit, Claudia and Pabst, Oliver},
  Title           = {The immune landscape of IgA induction in the gut},
  JournalTitle    = {Semin. Immunopathol.},
  Date            = {2021},
  DOI             = {10.1007/s00281-021-00879-4},
  Keywords        = {,CRC1382-Project B06,CRC1382-Project Q04},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {5},
  Pages           = {627--637},
  Volume          = {43}
}

@Article{Seki2007-iz,
  Author          = {Seki, Ekihiro and De Minicis, Samuele and Osterreicher,
                    Christoph H and Kluwe, Johannes and Osawa, Yosuke and
                    Brenner, David A and Schwabe, Robert F},
  Title           = {{TLR4} enhances {TGF-beta} signaling and hepatic
                    fibrosis},
  JournalTitle    = {Nat. Med.},
  Date            = {2007},
  DOI             = {10.1038/nm1663},
  Number          = {11},
  Pages           = {1324--1332},
  Volume          = {13}
}

@Article{Shalon2022,
  Author          = {Shalon, Dari and Culver, Rebecca Neal and Grembi,
                    Jessica A. and Folz, Jacob and Treit, Peter and
                    Dethlefsen, Les and Meng, Xiandong and Yaffe, Eitan and
                    Spencer, Sean and Shi, Handuo and Aranda-Dı́az, Andrés
                    and Patterson, Andrew D. and Triadafilopoulos, George and
                    Holmes, Susan P. and Mann, Matthias and Fiehn, Oliver and
                    Relman, David A. and Huang, Kerwyn Casey},
  Title           = {Profiling of the human intestinal microbiome and bile
                    acids under physiologic conditions using an ingestible
                    sampling device},
  JournalTitle    = {Microbiology},
  Date            = {2022},
  DOI             = {10.1101/2022.01.19.476920}
}

@Article{Shamji2019-rc,
  Author          = {Shamji, Mohamed H. and Thomsen, Irene and Layhadi,
                    Janice A. and Kappen, Jasper and Holtappels, Gabriële
                    and Sahiner, Umit and Switzer, Amy and Durham, Stephen R.
                    and Pabst, Oliver and Bachert, Claus},
  Title           = {Broad {IgG} repertoire in patients with chronic
                    rhinosinusitis with nasal polyps regulates
                    proinflammatory {IgE} responses},
  JournalTitle    = {J. Allergy Clin. Immun.},
  Date            = {2019},
  author+an:default = {10=equal;9=equal},
  DOI             = {10.1016/j.jaci.2019.02.001},
  Keywords        = {Pabst-Selection},
  Number          = {6},
  Pages           = {2086--2094.e2},
  Addendum        = equal,
  Volume          = {143}
}

@Article{Sharma2016-pu,
  Author          = {Sharma, Deepika and Kanneganti, Thirumala-Devi},
  Title           = {The cell biology of inflammasomes: {Mechanisms} of
                    inflammasome activation and regulation},
  JournalTitle    = {J. Cell Biol.},
  Date            = {2016},
  DOI             = {10.1083/jcb.201602089},
  Number          = {6},
  Pages           = {617--629},
  Volume          = {213}
}

@InCollection{Sharmila2018Pathogenesis,
  Author          = {Sharmila, Tirumale and Thomas, Tessy Anu},
  Title           = {Pathogenesis of Cholera: {Recent} Prospectives in Rapid
                    Detection and Prevention of Cholera},
  Date            = {2018},
  BookTitle       = {Bacterial Pathogenesis and Antibacterial Control},
  DOI             = {10.5772/intechopen.74071}
}

@Article{Sheth2007-xj,
  Author          = {Sheth, P. and Delos Santos, N. and Seth, A. and LaRusso,
                    N. F. and Rao, R. K.},
  Title           = {Lipopolysaccharide disrupts tight junctions in
                    cholangiocyte monolayers by a c-Src-, {TLR4}-, and
                    {LBP}-dependent mechanism},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2007},
  DOI             = {10.1152/ajpgi.00582.2006},
  Number          = {1},
  Pages           = {G308--G318},
  Volume          = {293}
}

@Article{Shetty2012,
  Author          = {Shetty, Shishir and Bruns, Tony and Weston, Christopher
                    J. and Stamataki, Zania and Oo, Ye H. and Long, Heather
                    M. and Reynolds, Gary M. and Pratt, Guy and Moss, Paul
                    and Jalkanen, Sirpa and Hubscher, Stefan G. and Lalor,
                    Patricia F. and Adams, David H.},
  Title           = {Recruitment mechanisms of primary and malignant B cells
                    to the human liver},
  JournalTitle    = {Hepatology},
  Date            = {2012},
  author+an:default = {1=equal;2=equal},
  Addendum        = equal,
  DOI             = {10.1002/hep.25790},
  Keywords        = {Bruns-Selection},
  Number          = {4},
  Pages           = {1521--1531},
  Volume          = {56}
}

@Article{Shiao2018,
  Author          = {Shiao, Meng-Shin and Chiablaem, Khajeelak and
                    Charoensawan, Varodom and Ngamphaiboon, Nuttapong and
                    Jinawath, Natini},
  Title           = {Emergence of Intrahepatic Cholangiocarcinoma: How
                    High-Throughput Technologies Expedite the Solutions for a
                    Rare Cancer Type},
  JournalTitle    = {Front. Genet.},
  Date            = {2018},
  DOI             = {10.3389/fgene.2018.00309},
  Volume          = {9}
}

@Article{Sips2018-rz,
  Author          = {Sips, Fianne L. P. and Eggink, Hannah M. and Hilbers,
                    Peter A. J. and Soeters, Maarten R. and Groen, Albert K.
                    and van Riel, Natal A. W.},
  Title           = {In Silico Analysis Identifies Intestinal Transit as a
                    Key Determinant of Systemic Bile Acid Metabolism},
  JournalTitle    = {Front. Physiol.},
  Date            = {2018},
  DOI             = {10.3389/fphys.2018.00631},
  Keywords        = {intestinal transit; mathematical modeling; plasma bile
                    acids; postprandial bile acid metabolism; postprandial
                    signaling},
  Pages           = {631},
  Volume          = {9}
}

@Article{Sistrunk2016Survival,
  Author          = {Sistrunk, Jeticia R. and Nickerson, Kourtney P. and
                    Chanin, Rachael B. and Rasko, David A. and Faherty,
                    Christina S.},
  Title           = {Survival of the Fittest: {How} Bacterial Pathogens
                    Utilize Bile To Enhance Infection},
  JournalTitle    = {Clin. Microbiol. Rev.},
  Date            = {2016-10},
  DOI             = {10.1128/cmr.00031-16},
  Number          = {4},
  Pages           = {819--836},
  Volume          = {29}
}

@Article{Siwczak2022-qo,
  Author          = {Siwczak, Fatina and Cseresnyes, Zoltan and Hassan,
                    Mohamed I.Abdelwahab and Aina, Kehinde Oluwasegun and
                    Carlstedt, Swen and Sigmund, Anke and Groger, Marko and
                    Surewaard, Bas G.J. and Werz, Oliver and Figge, Marc
                    Thilo and Tuchscherr, Lorena and Loffler, Bettina and
                    Mosig, Alexander S.},
  Title           = {Human macrophage polarization determines bacterial
                    persistence of Staphylococcus aureus in a
                    liver-on-chip-based infection model},
  JournalTitle    = {Biomaterials},
  Date            = {2022},
  DOI             = {10.1016/j.biomaterials.2022.121632},
  Pages           = {121632},
  Volume          = {287}
}

@Article{Siwy:465118,
  Author          = {Siwy, Justyna and Schanstra, Joost P. and Argiles, Angel
                    and Bakker, Stephan J.L. and Beige, Joachim and Boucek,
                    Petr and Brand, Korbinian and Delles, Christian and
                    Duranton, Flore and Fernandez-Fernandez, Beatriz and
                    Jankowski, Marie-Luise and Al Khatib, Mohammad and Kunt,
                    Thomas and Lajer, Maria and Lichtinghagen, Ralf and
                    Lindhardt, Morten and Maahs, David M and Mischak, Harald
                    and Mullen, William and Navis, Gerjan and Noutsou, Marina
                    and Ortiz, Alberto and Persson, Frederik and Petrie, John
                    R. and Roob, Johannes M. and Rossing, Peter and
                    Ruggenenti, Piero and Rychlik, Ivan and Serra, Andreas L.
                    and Snell-Bergeon, Janet and Spasovski, Goce and
                    Stojceva-Taneva, Olivera and Trillini, Matias and von der
                    Leyen, Heiko and Winklhofer-Roob, Brigitte M. and
                    Zürbig, Petra and Jankowski, Joachim},
  Title           = {Multicentre prospective validation of a urinary
                    peptidome-based classifier for the diagnosis of type 2
                    diabetic nephropathy},
  JournalTitle    = {Nephrol. Dial. Transplant.},
  Date            = {2014},
  DOI             = {10.1093/ndt/gfu039},
  Number          = {8},
  Pages           = {1563--1570},
  Volume          = {29}
}

@Article{Son2013Bacteria,
  Author          = {Son, Kwangmin and Guasto, Jeffrey S. and Stocker,
                    Roman},
  Title           = {Bacteria can exploit a flagellar buckling instability to
                    change direction},
  JournalTitle    = {Nat. Phys.},
  Date            = {2013-07-07},
  DOI             = {10.1038/nphys2676},
  Number          = {8},
  Pages           = {494--498},
  Volume          = {9}
}

@Article{Sonntag2018,
  Author          = {Sonntag, Roland and Giebeler, Nives and Nevzorova, Yulia
                    A. and Bangen, Jörg-Martin and Fahrenkamp, Dirk and
                    Lambertz, Daniela and Haas, Ute and Hu, Wei and Gassler,
                    Nikolaus and Cubero, Francisco Javier and Müller-Newen,
                    Gerhard and Abdallah, Ali T. and Weiskirchen, Ralf and
                    Ticconi, Fabio and Costa, Ivan G. and Barbacid, Mariano
                    and Trautwein, Christian and Liedtke, Christian},
  Title           = {Cyclin E1 and cyclin-dependent kinase 2 are critical for
                    initiation, but not for progression of hepatocellular
                    carcinoma},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2018},
  DOI             = {10.1073/pnas.1807155115},
  ids             = {sonntag2018a},
  Keywords        = {Liedtke-Selection,Nevzorova-Selection},
  Number          = {37},
  Pages           = {9282--9287},
  Volume          = {115}
}

@Article{Soppert2020-ry,
  Author          = {Soppert, Josefin and Lehrke, Michael and Marx, Nikolaus
                    and Jankowski, Joachim and Noels, Heidi},
  Title           = {Lipoproteins and lipids in cardiovascular disease:
                    {From} mechanistic insights to therapeutic targeting},
  JournalTitle    = {Adv. Drug Deliv. Rev.},
  Date            = {2020},
  DOI             = {10.1016/j.addr.2020.07.019},
  Pages           = {4--33},
  Volume          = {159}
}

@Article{Soppert2022-ab,
  Author          = {Soppert, Josefin and Frisch, Janina and Wirth, Julia and
                    Hemmers, Christian and Boor, Peter and Kramann, Rafael
                    and Vondenhoff, Sonja and Moellmann, Julia and Lehrke,
                    Michael and Hohl, Mathias and van der Vorst, Emiel P.C.
                    and Werner, Christian and Speer, Thimoteus and Maack,
                    Christoph and Marx, Nikolaus and Jankowski, Joachim and
                    Roma, Leticia Prates and Noels, Heidi},
  Title           = {A systematic review and meta-analysis of murine models
                    of uremic cardiomyopathy},
  JournalTitle    = {Kidney Int.},
  Date            = {2022},
  DOI             = {10.1016/j.kint.2021.10.025},
  Keywords        = {Noels-Selection},
  Number          = {2},
  Pages           = {256--273},
  Volume          = {101}
}

@Article{Speer:564845,
  Author          = {Speer, Thimoteus and Owala, Frederick O. and Holy, Erik
                    W. and Zewinger, Stephen and Frenzel, Felix L. and
                    Stähli, Barbara E. and Razavi, Marjan and Triem, Sarah
                    and Cvija, Hrvoje and Rohrer, Lucia and Seiler, Sarah and
                    Heine, Gunnar H. and Jankowski, Vera and Jankowski,
                    Joachim and Camici, Giovanni G. and Akhmedov, Alexander
                    and Fliser, Danilo and Lüscher, Thomas F. and Tanner,
                    Felix C.},
  Title           = {Carbamylated low-density lipoprotein induces endothelial
                    dysfunction},
  JournalTitle    = {Eur. Heart J.},
  Date            = {2014},
  DOI             = {10.1093/eurheartj/ehu111},
  Keywords        = {Jankowski-Selection},
  Number          = {43},
  Pages           = {3021--3032},
  Volume          = {35}
}

@Article{Stoeckius2017-bk,
  Author          = {Stoeckius, Marlon and Hafemeister, Christoph and
                    Stephenson, William and Houck-Loomis, Brian and
                    Chattopadhyay, Pratip K and Swerdlow, Harold and Satija,
                    Rahul and Smibert, Peter},
  Title           = {Simultaneous epitope and transcriptome measurement in
                    single cells},
  JournalTitle    = {Nat. Methods},
  Date            = {2017},
  DOI             = {10.1038/nmeth.4380},
  Number          = {9},
  Pages           = {865--868},
  Volume          = {14}
}

@Article{Stein_Thoeringer_2019,
  Author          = {Stein-Thoeringer, C. K. and Nichols, K. B. and Lazrak,
                    A. and Docampo, M. D. and Slingerland, A. E. and
                    Slingerland, J. B. and Clurman, A. G. and Armijo, G. and
                    Gomes, A. L. C. and Shono, Y. and Staffas, A. and Burgos
                    da Silva, M. and Devlin, S. M. and Markey, K. A. and
                    Bajic, D. and Pinedo, R. and Tsakmaklis, A. and Littmann,
                    E. R. and Pastore, A. and Taur, Y. and Monette, S. and
                    Arcila, M. E. and Pickard, A. J. and Maloy, M. and
                    Wright, R. J. and Amoretti, L. A. and Fontana, E. and
                    Pham, D. and Jamal, M. A. and Weber, D. and Sung, A. D.
                    and Hashimoto, D. and Scheid, C. and Xavier, J. B. and
                    Messina, J. A. and Romero, K. and Lew, M. and Bush, A.
                    and Bohannon, L. and Hayasaka, K. and Hasegawa, Y. and
                    Vehreschild, M. J. G. T. and Cross, J. R. and Ponce, D.
                    M. and Perales, M. A. and Giralt, S. A. and Jenq, R. R.
                    and Teshima, T. and Holler, E. and Chao, N. J. and Pamer,
                    E. G. and Peled, J. U. and van den Brink, M. R. M.},
  Title           = {Lactose drives \emph{Enterococcus} expansion to promote
                    graft-versus-host disease},
  JournalTitle    = {Science},
  Date            = {2019},
  DOI             = {10.1126/science.aax3760},
  Keywords        = {Vehreschild-Selection},
  Number          = {6469},
  Pages           = {1143--1149},
  Volume          = {366}
}

@Article{Vogt2016-tc,
  Author          = {Vogt, Anika and Reuken, Philipp A and Stengel, Sven and
                    Stallmach, Andreas and Bruns, Tony},
  Title           = {Dual-sugar tests of small intestinal permeability are
                    poor predictors of bacterial infections and mortality in
                    cirrhosis: {A} prospective study},
  JournalTitle    = {World J. Gastroenterol.},
  Date            = {2016},
  DOI             = {10.3748/wjg.v22.i11.3275},
  Number          = {11},
  Pages           = {3275},
  Volume          = {22}
}

@Article{Leonhardt2021-mj,
  Author          = {Leonhardt, Julia and Haider, Raphael S. and Sponholz,
                    Christoph and Leonhardt, Silke and Drube, Julia and
                    Spengler, Katrin and Mihaylov, Diana and Neugebauer,
                    Sophie and Kiehntopf, Michael and Lambert, Nevin A. and
                    Kortgen, Andreas and Bruns, Tony and Tacke, Frank and
                    Hoffmann, Carsten and Bauer, Michael and Heller, Regine},
  Title           = {Circulating Bile Acids in Liver Failure Activate {TGR5}
                    and Induce Monocyte Dysfunction},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jcmgh.2021.01.011},
  Number          = {1},
  Pages           = {25--40},
  Volume          = {12}
}

@Article{Stender2017-is,
  Author          = {Stender, Stefan and Kozlitina, Julia and Nordestgaard,
                    Børge G and Tybjærg-Hansen, Anne and Hobbs, Helen H and
                    Cohen, Jonathan C},
  Title           = {Adiposity amplifies the genetic risk of fatty liver
                    disease conferred by multiple loci},
  JournalTitle    = {Nat. Genet.},
  Date            = {2017},
  DOI             = {10.1038/ng.3855},
  Number          = {6},
  Pages           = {842--847},
  Volume          = {49}
}

@Article{Schupack2022-og,
  Author          = {Schupack, Daniel A. and Mars, Ruben A. T. and Voelker,
                    Dayne H. and Abeykoon, Jithma P. and Kashyap, Purna C.},
  Title           = {The promise of the gut microbiome as part of
                    individualized treatment strategies},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1038/s41575-021-00499-1},
  Number          = {1},
  Pages           = {7--25},
  Volume          = {19}
}

@Article{Stengel:787169,
  Author          = {Stengel, Sven and Quickert, Stefanie and Lutz, Philipp
                    and Ibidapo-Obe, Oluwatomi and Steube, Arndt and
                    Köse-Vogel, Nilay and Yarbakht, Melina and Reuken,
                    Philipp A. and Busch, Martin and Brandt, Annette and
                    Bergheim, Ina and Deshmukh, Sachin D. and Stallmach,
                    Andreas and Bruns, Tony},
  Title           = {Peritoneal Level of {CD206} Associates With Mortality
                    and an Inflammatory Macrophage Phenotype in Patients With
                    Decompensated Cirrhosis and Spontaneous Bacterial
                    Peritonitis},
  JournalTitle    = {Gastroenterology},
  Date            = {2020},
  DOI             = {10.1053/j.gastro.2020.01.029},
  Keywords        = {Bruns-Selection},
  Number          = {6},
  Pages           = {1745--1761},
  Volume          = {158}
}

@Article{Sternkopf2020-wf,
  Author          = {Sternkopf, Marieke and Nagy, Magdolna and Baaten,
                    Constance C.F.M.J. and Kuijpers, Marijke J.E. and
                    Tullemans, Bibian M.E. and Wirth, Julia and Theelen,
                    Wendy and Mastenbroek, Tom G. and Lehrke, Michael and
                    Winnerling, Benjamin and Baerts, Lesley and Marx,
                    Nikolaus and De Meester, Ingrid and Döring, Yvonne and
                    Cosemans, Judith M.E.M. and Daiber, Andreas and Steven,
                    Sebastian and Jankowski, Joachim and Heemskerk, Johan
                    W.M. and Noels, Heidi},
  Title           = {Native, Intact Glucagon-Like Peptide 1 Is a Natural
                    Suppressor of Thrombus Growth Under Physiological Flow
                    Conditions},
  JournalTitle    = { Arterioscl. Throm. Vas.},
  Date            = {2020},
  DOI             = {10.1161/atvbaha.119.313645},
  Keywords        = {Noels-Selection},
  Number          = {3},
  Pages           = {e65--e77},
  Volume          = {40}
}

@Article{Streidl:809963,
  Author          = {Streidl, Theresa and Karkossa, Isabel and Segura Muñoz,
                    Rafael R. and Eberl, Claudia and Zaufel, Alex and Plagge,
                    Johannes and Schmaltz, Robert and Schubert, Kristin and
                    Basic, Marijana and Schneider, Kai Markus and Afify,
                    Mamdouh and Trautwein, Christian and Tolba, René H. and
                    Stecher, Bärbel and Doden, Heidi L. and Ridlon, Jason M.
                    and Ecker, Josef and Moustafa, Tarek and von Bergen,
                    Martin and Ramer-Tait, Amanda E. and Clavel, Thomas},
  Title           = {The gut bacterium Extibacter muris produces secondary
                    bile acids and influences liver physiology in gnotobiotic
                    mice},
  JournalTitle    = {Gut microbes},
  Date            = {2021},
  DOI             = {10.1080/19490976.2020.1854008},
  Keywords        = {Clavel-Selection,CRC1382-Project A05,CRC1382-Project
                    Q02,CRC1382-Project A06,CRC1382-Project
                    A08,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {1--21},
  Volume          = {13}
}

@Article{Tropini2018-xc,
  Author          = {Tropini, Carolina and Moss, Eli Lin and Merrill, Bryan
                    Douglas and Ng, Katharine Michelle and Higginbottom,
                    Steven Kyle and Casavant, Ellen Pun and Gonzalez, Carlos
                    Gutierrez and Fremin, Brayon and Bouley, Donna Michelle
                    and Elias, Joshua Eric and Bhatt, Ami Siddharth and
                    Huang, Kerwyn Casey and Sonnenburg, Justin Laine},
  Title           = {Transient Osmotic Perturbation Causes Long-Term
                    Alteration to the Gut Microbiota},
  JournalTitle    = {Cell},
  Date            = {2018},
  DOI             = {10.1016/j.cell.2018.05.008},
  Number          = {7},
  Pages           = {1742--1754.e17},
  Volume          = {173}
}

@Article{nature-editorial-2016,
  Title           = {The plight of young scientists},
  JournalTitle    = {Nature},
  Date            = {2016},
  DOI             = {10.1038/538443a},
  Number          = {7626},
  Pages           = {443--443},
  Shorthand       = {Nature 538},
  Volume          = {538}
}

@Article{Strnad2007,
  Author          = {Strnad, Pavel and Harada, Masaru and Siegel, Matthew and
                    Terkeltaub, Robert A. and Graham, Robert M. and Khosla,
                    Chaitan and Omary, M. Bishr},
  Title           = {Transglutaminase 2 Regulates {Mallory} Body Inclusion
                    Formation and Injury-Associated Liver Enlargement},
  JournalTitle    = {Gastroenterology},
  Date            = {2007},
  DOI             = {10.1053/j.gastro.2007.02.020},
  Number          = {4},
  Pages           = {1515--1526},
  Volume          = {132}
}

@Article{Strnad2008,
  Author          = {Strnad, Pavel and Tao, Guo–Zhong and Zhou, Qin and
                    Harada, Masaru and Toivola, Diana M. and Brunt, Elizabeth
                    M. and Omary, M. Bishr},
  Title           = {Keratin Mutation Predisposes to Mouse Liver Fibrosis and
                    Unmasks Differential Effects of the Carbon Tetrachloride
                    and Thioacetamide Models},
  JournalTitle    = {Gastroenterology},
  Date            = {2008},
  DOI             = {10.1053/j.gastro.2008.01.035},
  Number          = {4},
  Pages           = {1169--1179},
  Volume          = {134}
}

@Article{Strnad2010,
  Author          = {Strnad, Pavel and Zhou, Qin and Hanada, Shinichiro and
                    Lazzeroni, Laura C. and Zhong, Bi Hui and So, Phillip and
                    Davern, Timothy J. and Lee, William M. and Omary, M.
                    Bishr},
  Title           = {Keratin Variants Predispose to Acute Liver Failure and
                    Adverse Outcome: {Race} and Ethnic Associations},
  JournalTitle    = {Gastroenterology},
  Date            = {2010},
  DOI             = {10.1053/j.gastro.2010.06.007},
  Number          = {3},
  Pages           = {828--835.e3},
  Volume          = {139}
}

@Article{Strnad2012,
  Author          = {Strnad, Pavel and Kucukoglu, Ozlem and Lunova, Mariia
                    and Guldiken, Nurdan and Lienau, Tim C. and Stickel,
                    Felix and Omary, M. Bishr},
  Title           = {Non-Coding Keratin Variants Associate with Liver
                    Fibrosis Progression in Patients with Hemochromatosis},
  JournalTitle    = {PLoS ONE},
  Date            = {2012},
  DOI             = {10.1371/journal.pone.0032669},
  Editor          = {Aldabe, Rafael},
  Number          = {3},
  Pages           = {e32669},
  Volume          = {7}
}

@Article{Strnad2020-wq,
  Author          = {Strnad, Pavel and McElvaney, Noel G. and Lomas, David
                    A.},
  Title           = {Alpha\textsubscript{1}-Antitrypsin Deficiency},
  JournalTitle    = {N. Engl. J. Med.},
  Date            = {2020},
  DOI             = {10.1056/nejmra1910234},
  Keywords        = {Strnad-Selection},
  Number          = {15},
  Pages           = {1443--1455},
  Volume          = {382}
}

@Article{Strnad2022-nt,
  Author          = {Strnad, Pavel and Mandorfer, Mattias and Choudhury,
                    Gourab and Griffiths, William and Trautwein, Christian
                    and Loomba, Rohit and Schluep, Thomas and Chang, Ting and
                    Yi, Min and Given, Bruce D. and Hamilton, James C. and
                    San Martin, Javier and Teckman, Jeffery H.},
  Title           = {Fazirsiran for Liver Disease Associated with
                    Alpha\textsubscript{1}-Antitrypsin Deficiency},
  JournalTitle    = {N. Engl. J. Med.},
  Date            = {2022},
  DOI             = {10.1056/nejmoa2205416},
  Keywords        = {Strnad-Selection,Trautwein-Selection},
  pmid            = {35748699},
  Number          = {6},
  Pages           = {514--524},
  Volume          = {387}
}

@Article{Strnad:785992,
  Author          = {Strnad, Pavel and Buch, Stephan and Hamesch, Karim and
                    Fischer, Janett and Rosendahl, Jonas and Schmelz, Renate
                    and Brueckner, Stefan and Brosch, Mario and Heimes,
                    Carolin V. and Woditsch, Vivien and Scholten, David and
                    Nischalke, Hans Dieter and Janciauskiene, Sabina and
                    Mandorfer, Mattias and Trauner, Michael and Way, Michael
                    J and McQuillin, Andrew and Reichert, Matthias C and
                    Krawczyk, Marcin and Casper, Markus and Lammert, Frank
                    and Braun, Felix and von Schönfels, Witigo and Hinz,
                    Sebastian and Burmeister, Greta and Hellerbrand, Claus
                    and Teufel, Andreas and Feldman, Alexandra and
                    Schattenberg, Joern M and Bantel, Heike and Pathil, Anita
                    and Demir, Muenevver and Kluwe, Johannes and Boettler,
                    Tobias and Ridinger, Monika and Wodarz, Norbert and
                    Soyka, Michael and Rietschel, Marcella and Kiefer, Falk
                    and Weber, Thomas and Marhenke, Silke and Vogel, Arndt
                    and Hinrichsen, Holger and Canbay, Ali and Schlattjan,
                    Martin and Sosnowsky, Katharina and Sarrazin, Christoph
                    and von Felden, Johann and Geier, Andreas and Deltenre,
                    Pierre and Sipos, Bence and Schafmayer, Clemens and
                    Nothnagel, Michael and Aigner, Elmar and Datz, Christian
                    and Stickel, Felix and Morgan, Marsha Yvonne and Hampe,
                    Jochen and Berg, Thomas and Trautwein, Christian},
  Title           = {Heterozygous carriage of the alpha1-antitrypsin {Pi*Z}
                    variant increases the risk to develop liver cirrhosis},
  JournalTitle    = {Gut},
  Addendum        = equal,
  Date            = {2018},
  author+an:default = {1=equal;2=equal;3=equal},
  DOI             = {10.1136/gutjnl-2018-316228},
  Keywords        = {Strnad-Selection,Trautwein-Selection},
  Number          = {6},
  Pages           = {1099--1107},
  Volume          = {68}
}

@Article{Strowig2012,
  Author          = {Strowig, Till and Henao-Mejia, Jorge and Elinav, Eran
                    and Flavell, Richard},
  Title           = {Inflammasomes in health and disease},
  JournalTitle    = {Nature},
  DOI             = {10.1038/nature10759},
  Keywords        = {Caspase 1/metabolism; *Disease; *Health; Humans;
                    Immunity,Mucosal/immunology;
                    Inflammasomes/chemistry/*immunology/*metabolism;
                    Inflammation/immunology/metabolism/pathology; Metabolic
                    Syndrome/metabolism/pathology},
  Number          = {7381},
  Pages           = {278--286},
  Volume          = {481}
}

@Article{Suez2014-ii,
  Author          = {Suez, Jotham and Korem, Tal and Zeevi, David and
                    Zilberman-Schapira, Gili and Thaiss, Christoph A. and
                    Maza, Ori and Israeli, David and Zmora, Niv and Gilad,
                    Shlomit and Weinberger, Adina and Kuperman, Yael and
                    Harmelin, Alon and Kolodkin-Gal, Ilana and Shapiro, Hagit
                    and Halpern, Zamir and Segal, Eran and Elinav, Eran},
  Title           = {Artificial sweeteners induce glucose intolerance by
                    altering the gut microbiota},
  JournalTitle    = {Nature},
  Date            = {2014},
  DOI             = {10.1038/nature13793},
  Number          = {7521},
  Pages           = {181--186},
  Volume          = {514}
}

@Article{Suchy1981-se,
  Author          = {Suchy, Frederick J. and Balistreri, William F. and
                    Heubi, James E. and Searcy, John E. and Levin, Ron S.},
  Title           = {Physiologic cholestasis: {Elevation} of the primary
                    serum bile acid concentrations in normal infants},
  JournalTitle    = {Gastroenterology},
  Date            = {1981},
  DOI             = {10.1016/0016-5085(81)90078-0},
  Number          = {5},
  Pages           = {1037--1041},
  Volume          = {80}
}

@Article{Sunami2012,
  Author          = {Sunami, Yoshiaki and Leithäuser, Frank and Gul, Sarah
                    and Fiedler, Katja and Güldiken, Nurdan and Espenlaub,
                    Sigrid and Holzmann, Karl-Heinz and Hipp, Nora and
                    Sindrilaru, Anca and Luedde, Tom and Baumann, Bernd and
                    Wissel, Sebastian and Kreppel, Florian and Schneider,
                    Marion and Scharffetter-Kochanek, Karin and Kochanek,
                    Stefan and Strnad, Pavel and Wirth, Thomas},
  Title           = {Hepatic activation of {IKK/NFκB} signaling induces
                    liver fibrosis via macrophage-mediated chronic
                    inflammation},
  JournalTitle    = {Hepatology},
  Date            = {2012},
  DOI             = {10.1002/hep.25711},
  Number          = {3},
  Pages           = {1117--1128},
  Volume          = {56}
}

@Article{Sutti:784588,
  Author          = {Sutti, Salvatore and Bruzzì, Stefania and Heymann,
                    Felix and Liepelt, Anke and Krenkel, Oliver and Toscani,
                    Alberto and Ramavath, Naresh and Cotella, Diego and
                    Albano, Emanuele and Tacke, Frank},
  Title           = {{CX}3{CR}1 Mediates the Development of Monocyte-Derived
                    Dendritic Cells during Hepatic Inflammation},
  JournalTitle    = {Cells},
  Date            = {2019},
  DOI             = {10.3390/cells8091099},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {9},
  Pages           = {1099},
  Volume          = {8}
}

@Article{Szabo:540941,
  Author          = {Szabo, Sandra and Wögenstein, Karl L. and
                    Österreicher, Christoph H. and Guldiken, Nurdan and
                    Chen, Yu and Doler, Carina and Wiche, Gerhard and Boor,
                    Peter and Haybaeck, Johannes and Strnad, Pavel and Fuchs,
                    Peter},
  Title           = {Epiplakin attenuates experimental mouse liver injury by
                    chaperoning keratin reorganization},
  JournalTitle    = {J. Hepatol.},
  Date            = {2015},
  DOI             = {10.1016/j.jhep.2015.01.007},
  Number          = {6},
  Pages           = {1357--1366},
  Volume          = {62}
}

@Article{Tabibian2013-qp,
  Author          = {Tabibian, James H and Macura, Slobodan I and O'Hara,
                    Steven P and Fidler, Jeff L and Glockner, James F and
                    Takahashi, Naoki and Lowe, Val J and Kemp, Bradley J and
                    Mishra, Prasanna K and Tietz, Pamela S and Splinter,
                    Patrick L and Trussoni, Christy E and LaRusso, Nicholas
                    F},
  Title           = {Micro-computed tomography and nuclear magnetic resonance
                    imaging for noninvasive, live-mouse cholangiography},
  JournalTitle    = {Lab. Invest.},
  Date            = {2013},
  DOI             = {10.1038/labinvest.2013.52},
  Number          = {6},
  Pages           = {733--743},
  Volume          = {93}
}

@Article{Tacke:163412,
  Author          = {Tacke, Frank and Alvarez, David and Kaplan, Theodore J.
                    and Jakubzick, Claudia and Spanbroek, Rainer and Llodra,
                    Jaime and Garin, Alexandre and Liu, Jianhua and Mack,
                    Matthias and van Rooijen, Nico and Lira, Sergio A. and
                    Habenicht, Andreas J. and Randolph, Gwendalyn J.},
  Title           = {Monocyte subsets differentially employ {CCR2,} {CCR5,}
                    and {CX3CR1} to accumulate within atherosclerotic
                    plaques},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2007},
  DOI             = {10.1172/jci28549},
  Keywords        = {Tacke-Selection},
  Number          = {1},
  Pages           = {185--194},
  ShortJournal    = {JCI},
  Volume          = {117}
}

@Article{Tacke:195289,
  Author          = {Tacke, Frank and Ginhoux, Florent and Jakubzick, Claudia
                    and van Rooijen, Nico and Merad, Miriam and Randolph,
                    Gwendalyn J.},
  Title           = {Immature monocytes acquire antigens from other cells in
                    the bone marrow and present them to T cells after
                    maturing in the periphery},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2006},
  DOI             = {10.1084/jem.20052119},
  Keywords        = {Tacke-Selection},
  Number          = {3},
  Pages           = {583--597},
  ShortJournal    = {JEM},
  Volume          = {203}
}

@Article{Tacke:828492,
  Author          = {Tacke, Frank and Weiskirchen, Ralf},
  Title           = {Non-alcoholic fatty liver disease
                    ({NAFLD})/non-alcoholic steatohepatitis ({NASH})-related
                    liver fibrosis},
  JournalTitle    = {Ann. Transl. Med.},
  Date            = {2021},
  DOI             = {10.21037/atm-20-4354},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {8},
  Pages           = {729},
  ShortJournal    = {ATM},
  Subtitle        = {Mechanisms, treatment and prevention},
  Volume          = {9}
}

@Article{Tag2015-yq,
  Author          = {Tag, Carmen G. and Sauer-Lehnen, Sibille and
                    Weiskirchen, Sabine and Borkham-Kamphorst, Erawan and
                    Tolba, René H. and Tacke, Frank and Weiskirchen, Ralf},
  Title           = {Bile Duct Ligation in Mice: {Induction} of Inflammatory
                    Liver Injury and Fibrosis by Obstructive Cholestasis},
  JournalTitle    = {J. Vis. Exp.},
  Date            = {2015},
  DOI             = {10.3791/52438},
  Number          = {96}
}

@Article{Tapper2018-ze,
  Author          = {Tapper, Elliot B and Parikh, Neehar D},
  Title           = {Mortality due to cirrhosis and liver cancer in the
                    United States, 1999-2016: {Observational} study},
  JournalTitle    = {BMJ},
  Date            = {2018},
  DOI             = {10.1136/bmj.k2817},
  Pages           = {k2817},
  Volume          = {362}
}

@Article{Thiel2017,
  Author          = {Thiel, C and Cordes, H and Baier, V and Blank, LM and
                    Kuepfer, L},
  Title           = {Multiscale modeling reveals inhibitory and stimulatory
                    effects of caffeine on acetaminophen‐induced toxicity
                    in humans},
  JournalTitle    = {CPT: Pharmacomet. Syst. Pharmacol.},
  Date            = {2017},
  DOI             = {10.1002/psp4.12153},
  Number          = {2},
  Pages           = {136--146},
  Volume          = {6}
}

@Article{Thiel:659692,
  Author          = {Thiel, Christoph and Cordes, Henrik and Conde, Isabel
                    and Castell, José Vicente and Blank, Lars Mathias and
                    Kuepfer, Lars},
  Title           = {Model-based contextualization of in vitro toxicity data
                    quantitatively predicts in vivo drug response in
                    patients},
  JournalTitle    = {Arch. Toxicol.},
  Date            = {2016},
  DOI             = {10.1007/s00204-016-1723-x},
  Number          = {2},
  Pages           = {865--883},
  Volume          = {91}
}

@Article{Thiele:791933,
  Author          = {Thiele, Maja and Hugger, Mie Balle and Kim, Yongsoo and
                    Rautou, Pierre-Emmanuel and Elkrief, Laure and Jansen,
                    Christian and Verlinden, Wim and Allegretti, Giulia and
                    Israelsen, Mads and Stefanescu, Horia and Piscaglia,
                    Fabio and García-Pagán, Juan Carlos and Franque, Sven
                    and Berzigotti, Annalisa and Castera, Laurent and Jeong,
                    Woo Kyoung and Trebicka, Jonel and Krag, Aleksander},
  Title           = {2D shear wave liver elastography by aixplorer to detect
                    portal hypertension in cirrhosis: an individual patient
                    data meta-analysis},
  JournalTitle    = {Liver Int.},
  Date            = {2020},
  DOI             = {10.1111/liv.14439},
  Keywords        = {,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {6},
  Pages           = {1435--1446},
  Volume          = {40}
}

@Article{Thogersen2020-iu,
  Author          = {Thøgersen, Rebekka and Rasmussen, Martin Krøyer and
                    Sundekilde, Ulrik K. and Goethals, Sophie A. and Van
                    Hecke, Thomas and Vossen, Els and De Smet, Stefaan and
                    Bertram, Hanne Christine},
  Title           = {Background Diet Influences {TMAO} Concentrations
                    Associated with Red Meat Intake without Influencing
                    Apparent Hepatic {TMAO}-Related Activity in a Porcine
                    Model},
  JournalTitle    = {Metabolites},
  Date            = {2020},
  DOI             = {10.3390/metabo10020057},
  Number          = {2},
  Pages           = {57},
  Volume          = {10}
}

@Article{DAmico2006,
  Author          = {D’Amico, Gennaro and Garcia-Tsao, Guadalupe and
                    Pagliaro, Luigi},
  Title           = {Natural history and prognostic indicators of survival in
                    cirrhosis: {A} systematic review of 118 studies},
  JournalTitle    = {J. Hepatol.},
  Date            = {2006},
  DOI             = {10.1016/j.jhep.2005.10.013},
  Number          = {1},
  Pages           = {217--231},
  Volume          = {44}
}

@Article{Tilstam2020-ov,
  Author          = {Tilstam, Pathricia V. and Soppert, Josefin and Hemmers,
                    Christian and Harlacher, Eva and Döring, Yvonne and van
                    der Vorst, Emiel P.C. and Schulte, Corinna and
                    Alampour-Rajabi, Setareh and Theelen, Wendy and Asare,
                    Yaw and de Winther, Menno P.J. and Lawrence, Toby and
                    Bernhagen, Jürgen and Schober, Andreas and Zernecke,
                    Alma and Jankowski, Joachim and Weber, Christian and
                    Noels, Heidi},
  Title           = {Non-activatable mutant of inhibitor of kappa B kinase α
                    {(IKKα)} exerts vascular site-specific effects on
                    atherosclerosis in Apoe-deficient mice},
  JournalTitle    = {Atherosclerosis},
  Date            = {2020},
  DOI             = {10.1016/j.atherosclerosis.2019.10.023},
  Keywords        = {Noels-Selection},
  Pages           = {23--30},
  Volume          = {292}
}

@Article{Tiso2021-dd,
  Author          = {Tiso, Till and Narancic, Tanja and Wei, Ren and Pollet,
                    Eric and Beagan, Niall and Schröder, Katja and Honak,
                    Annett and Jiang, Mengying and Kenny, Shane T. and
                    Wierckx, Nick and Perrin, Rémi and Avérous, Luc and
                    Zimmermann, Wolfgang and O'Connor, Kevin and Blank, Lars
                    M.},
  Title           = {Towards bio-upcycling of polyethylene terephthalate},
  JournalTitle    = {Metab. Eng.},
  Date            = {2021},
  DOI             = {10.1016/j.ymben.2021.03.011},
  Keywords        = {Blank-Selection},
  Pages           = {167--178},
  Volume          = {66}
}

@Article{Tiso2022-fq,
  Author          = {Tiso, Till and Winter, Benedikt and Wei, Ren and Hee,
                    Johann and de Witt, Jan and Wierckx, Nick and Quicker,
                    Peter and Bornscheuer, Uwe T and Bardow, André and
                    Nogales, Juan and Blank, Lars M.},
  Title           = {The metabolic potential of plastics as biotechnological
                    carbon sources - Review and targets for the future},
  JournalTitle    = {Metab. Eng.},
  Date            = {2022},
  DOI             = {10.1016/j.ymben.2021.12.006},
  Keywords        = {Biotechnological upcycling; Global warming impact;
                    Metabolic pathways; Plastics; Theoretical yield},
  Pages           = {77--98},
  Volume          = {71}
}

@Article{Tolle2005,
  Author          = {Tölle, Markus and Levkau, Bodo and Keul, Petra and
                    Brinkmann, Volker and Giebing, Günter and Schönfelder,
                    Gilbert and Schäfers, Michael and Lipinski, Karin von
                    Wnuck and Jankowski, Joachim and Jankowski, Vera and
                    Chun, Jerold and Zidek, Walter and Giet, Markus Van der},
  Title           = {Immunomodulator {FTY720} Induces {eNOS}-Dependent
                    Arterial Vasodilatation via the Lysophospholipid Receptor
                    {S1P3}},
  JournalTitle    = {Circ. Res.},
  Date            = {2005},
  DOI             = {10.1161/01.res.0000164321.91452.00},
  Number          = {8},
  Pages           = {913--920},
  Volume          = {96}
}

@Article{Grognot2015,
  Author          = {Grognot, Marianne and Gallot, Guilhem},
  Title           = {Quantitative measurement of permeabilization of living
                    cells by terahertz attenuated total reflection},
  JournalTitle    = {Appl. Phys. Lett.},
  Date            = {2015},
  DOI             = {10.1063/1.4930168},
  Keywords        = {Grognot-Selection},
  Number          = {10},
  Pages           = {103702},
  Volume          = {107}
}

@Article{Grognot2017-bb,
  Author          = {Grognot, Marianne and Gallot, Guilhem},
  Title           = {Relative Contributions of Core Protein and Solvation
                    Shell in the Terahertz Dielectric Properties of Protein
                    Solutions},
  JournalTitle    = {J. Phys. Chem. B},
  Date            = {2017},
  DOI             = {10.1021/acs.jpcb.7b06442},
  Keywords        = {Grognot-Selection},
  Number          = {41},
  Pages           = {9508--9512},
  Volume          = {121}
}

@Article{Azan2020-aa,
  Author          = {Azan, Antoine and Grognot, Marianne and
                    García-Sánchez, Tomás and Descamps, Lucie and
                    Untereiner, Valérie and Piot, Olivier and Gallot,
                    Guilhem and Mir, Lluis M.},
  Title           = {Monitoring the molecular composition of live cells
                    exposed to electric pulses via label-free optical
                    methods},
  JournalTitle    = {Sci. Rep.},
  Date            = {2020},
  DOI             = {10.1038/s41598-020-67402-x},
  Keywords        = {Grognot-Selection},
  Number          = {1},
  Volume          = {10}
}

@Article{Fonseca2000-xa,
  Author          = {Fonseca, A and Fell, J W and Kurtzman, C P and
                    Spencer-Martins, I},
  Title           = {Candida tartarivorans sp. nov., an anamorphic
                    ascomycetous yeast with the capacity to degrade L(+)- and
                    meso-tartaric acid.},
  JournalTitle    = {Int. J. Syst. Evol. Micr.},
  Date            = {2000},
  DOI             = {10.1099/00207713-50-1-389},
  Number          = {1},
  Pages           = {389--394},
  Volume          = {50}
}

@Article{Hong2019-eq,
  Author          = {Hong, Mengnan and Li, Jing and Chen, Yuwen},
  Title           = {Characterization of tolerance and multi‐enzyme
                    activities in non \emph{Saccharomyces} yeasts isolated
                    from {Vidal} blanc icewine fermentation},
  JournalTitle    = {J. Food Biochem.},
  Date            = {2019},
  DOI             = {10.1111/jfbc.13027},
  Number          = {11},
  Pages           = {e13027},
  Volume          = {43}
}

@Article{Burbidge2021-ow,
  Author          = {Burbidge, Crista Ann and Ford, Christopher Michael and
                    Melino, Vanessa Jane and Wong, Darren Chern Jan and Jia,
                    Yong and Jenkins, Colin Leslie Dow and Soole, Kathleen
                    Lydia and Castellarin, Simone Diego and Darriet, Philippe
                    and Rienth, Markus and Bonghi, Claudio and Walker, Robert
                    Peter and Famiani, Franco and Sweetman, Crystal},
  Title           = {Biosynthesis and Cellular Functions of Tartaric Acid in
                    Grapevines},
  JournalTitle    = {Front. Plant Sci.},
  Date            = {2021},
  DOI             = {10.3389/fpls.2021.643024},
  Pages           = {643024},
  Volume          = {12}
}

@Article{Costa-Silva2015-oj,
  Author          = {Costa-Silva, Bruno and Aiello, Nicole M. and Ocean,
                    Allyson J. and Singh, Swarnima and Zhang, Haiying and
                    Thakur, Basant Kumar and Becker, Annette and Hoshino,
                    Ayuko and Mark, Milica Tešić and Molina, Henrik and
                    Xiang, Jenny and Zhang, Tuo and Theilen, Till-Martin and
                    García-Santos, Guillermo and Williams, Caitlin and
                    Ararso, Yonathan and Huang, Yujie and Rodrigues, Gonçalo
                    and Shen, Tang-Long and Labori, Knut Jørgen and Lothe,
                    Inger Marie Bowitz and Kure, Elin H. and Hernandez,
                    Jonathan and Doussot, Alexandre and Ebbesen, Saya H. and
                    Grandgenett, Paul M. and Hollingsworth, Michael A. and
                    Jain, Maneesh and Mallya, Kavita and Batra, Surinder K.
                    and Jarnagin, William R. and Schwartz, Robert E. and
                    Matei, Irina and Peinado, Héctor and Stanger, Ben Z. and
                    Bromberg, Jacqueline and Lyden, David},
  Title           = {Pancreatic cancer exosomes initiate pre-metastatic niche
                    formation in the liver},
  JournalTitle    = {Nat. Cell Biol.},
  Date            = {2015},
  DOI             = {10.1038/ncb3169},
  Number          = {6},
  Pages           = {816--826},
  Volume          = {17}
}

@Article{Torow2022-jm,
  Author          = {Torow, N and Li, R and Hitch, T and Mingels, C and
                    Bounny, S al and van Best, N and Stange, Eva-Lena and
                    Benabid, A and Rüttger, L and Gadermayr, M and Runge, S
                    and Treichel, N and Merhof, D and Rosshart, S and
                    Jehmlich, N and von Bergen, M. and Heymann, F and Clavel,
                    Thomas and Tacke, F. and Lelouard, H and Costa, Ivan and
                    Hornef, Mathias W.},
  Title           = {Neonatal Peyer’s patch {cDC} activation as a pacemaker
                    of postnatal immune maturation},
  JournalTitle    = {bioRxiv},
  Date            = {2022},
  DOI             = {10.1101/2022.03.03.482839},
  Keywords        = {Hornef-Selection},
  PubState        = {preprint}
}

@Article{Kister2022,
  Author          = {Kister, Bastian and Viehof, Alina and Rolle-Kampczyk,
                    Ulrike and Schwentker, Annika and Treichel, Nicole and
                    Jennings, Susan and Wirtz, Theresa H. and Blank, Lars M.
                    and Hornef, Mathias W. and von Bergen, Martin and Clavel,
                    Tom and Kuepfer, Lars},
  Title           = {A physiologically based model of bile acid metabolism in
                    mice},
  JournalTitle    = {bioRxiv},
  Date            = {2022},
  DOI             = {10.1101/2022.11.10.515857},
  PubState        = {submitted}
}

@Article{Torow:566898,
  Author          = {Torow, Natalia and Yu, Kai and Hassani, Kasra and
                    Freitag, Jenny and Schulz, Olga and Basic, Marijana and
                    Brennecke, Anne and Sparwasser, Tim and Wagner, Norbert
                    and Bleich, André and Lochner, Matthias and Weiss,
                    Siegfried and Förster, Reinhold and Pabst, Oliver and
                    Hornef, Mathias W.},
  Title           = {Active suppression of intestinal {CD4+TCRαβ+}
                    T-lymphocyte maturation during the postnatal period},
  JournalTitle    = {Nat. Commun.},
  Date            = {2015},
  DOI             = {10.1038/ncomms8725},
  ids             = {Torow2015-ng},
  Keywords        = {Hornef-Selection},
  Number          = {1},
  Pages           = {7725},
  Volume          = {6}
}

@Article{Torres:787066,
  Author          = {Torres, Sandra and Abdullah, Zeinab and Brol, Maximilian
                    J. and Hellerbrand, Claus and Fernandez, Mercedes and
                    Fiorotto, Romina and Klein, Sabine and Königshofer,
                    Philipp and Liedtke, Christian and Lotersztajn, Sophie
                    and Nevzorova, Yulia A. and Schierwagen, Robert and
                    Reiberger, Thomas and Uschner, Frank Erhard and Tacke,
                    Frank and Weiskirchen, Ralf and Trebicka, Jonel},
  Title           = {Recent Advances in Practical Methods for Liver Cell
                    Biology},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2020},
  DOI             = {10.3390/ijms21062027},
  Keywords        = {,CRC1382-Project A02,CRC1382-Project Q03,CRC1382-Project
                    A02,CRC1382-Project A09,CRC1382-Project
                    B05,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {6},
  Pages           = {2027},
  Subtitle        = {A Short Overview},
  Volume          = {21}
}

@Article{Torres:834274,
  Author          = {Torres, Sandra and Brol, Maximilian J. and Magdaleno,
                    Fernando and Schierwagen, Robert and Uschner, Frank E.
                    and Klein, Sabine and Ortiz, Cristina and Tyc, Olaf and
                    Bachtler, Nadine and Stunden, James and Bertheloot,
                    Damien and Kitanovic, Ana and Sanchez, Brian and Schrum,
                    Jacob and Roush, William R. and Franchi, Luigi and Byth,
                    Kate and Latz, Eicke and Trebicka, Jonel},
  Title           = {The Specific {NLRP}3 Antagonist {IFM}-514 Decreases
                    Fibrosis and Inflammation in Experimental Murine
                    Non-Alcoholic Steatohepatitis},
  JournalTitle    = {Front. Mol. Biosci.},
  Date            = {2021},
  DOI             = {10.3389/fmolb.2021.715765},
  Keywords        = {,CRC1382-Project A09,CRC1382-Project A09,CRC1382-Project
                    A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {715765},
  Volume          = {8}
}

@Article{TorresRendon:483748,
  Author          = {Torres‐Rendon, Jose Guillermo and Femmer, Tim and De
                    Laporte, Laura and Tigges, Thomas and Rahimi, Khosrow and
                    Gremse, Felix and Zafarnia, Sara and Lederle, Wiltrud and
                    Ifuku, Shinsuke and Wessling, Matthias and Hardy, John G.
                    and Walther, Andreas},
  Title           = {Bioactive Gyroid Scaffolds Formed by Sacrificial
                    Templating of Nanocellulose and Nanochitin Hydrogels as
                    Instructive Platforms for Biomimetic Tissue Engineering},
  JournalTitle    = {Adv. Mater.},
  Date            = {2015},
  DOI             = {10.1002/adma.201405873},
  Keywords        = {Lederle-Selection},
  Number          = {19},
  Pages           = {2989--2995},
  Volume          = {27}
}

@Article{Toy2011-ke,
  Author          = {Toy, Elaine and Balasubramanian, Sripriya and Selmi,
                    Carlo and Li, Chin-Shang and Bowlus, Christopher L},
  Title           = {The prevalence, incidence and natural history of primary
                    sclerosing cholangitis in an ethnically diverse
                    population},
  JournalTitle    = {BMC Gastroenterol.},
  Date            = {2011},
  DOI             = {10.1186/1471-230x-11-83},
  Number          = {1},
  Pages           = {83},
  Volume          = {11}
}

@Article{Tran2019Flagellin,
  Author          = {Tran, Hao Q. and Ley, Ruth E. and Gewirtz, Andrew T. and
                    Chassaing, Benoit},
  Title           = {Flagellin-elicited adaptive immunity suppresses
                    flagellated microbiota and vaccinates against chronic
                    inflammatory diseases},
  JournalTitle    = {Nat. Commun.},
  Date            = {2019-12},
  DOI             = {10.1038/s41467-019-13538-y},
  Number          = {1},
  Pages           = {5650},
  Volume          = {10}
}

@Article{Trauner1999-zw,
  Author          = {Trauner, Michael and Fickert, Peter and Stauber, Rudolf
                    E},
  Title           = {Inflammation-induced cholestasis},
  JournalTitle    = {J. Gastroenterol. Hepatol.},
  Date            = {1999},
  DOI             = {10.1046/j.1440-1746.1999.01982.x},
  Number          = {10},
  Pages           = {946--959},
  Volume          = {14}
}

@Article{Trebicka2013,
  Author          = {Trebicka, Jonel and Anadol, Evrim and Elfimova, Natalia
                    and Strack, Ingo and Roggendorf, Michael and Viazov,
                    Sergei and Wedemeyer, Inga and Drebber, Uta and
                    Rockstroh, Jürgen and Sauerbruch, Tilman and Dienes,
                    Hans-Peter and Odenthal, Margarete},
  Title           = {Hepatic and serum levels of {miR}-122 after chronic
                    {HCV}-induced fibrosis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2013},
  DOI             = {10.1016/j.jhep.2012.10.015},
  Number          = {2},
  Pages           = {234--239},
  Volume          = {58}
}

@Article{Trebicka2016,
  Author          = {Trebicka, Jonel and von Heydebrand, Matthias and
                    Lehmann, Jennifer and Tofteng, Flemming and Busk, Troels
                    and Jensen, Helle Lone and Rohde, Johan and Reiberger,
                    Thomas and Mortensen, Christian and Schierwagen, Robert
                    and Klein, Sabine and Møller, Søren and Bendtsen,
                    Flemming and Krag, Aleksander},
  Title           = {Assessment of response to beta-blockers by expression of
                    {βArr2} and {RhoA/ROCK2} in antrum mucosa in cirrhotic
                    patients},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2016.01.022},
  Number          = {6},
  Pages           = {1265--1273},
  Volume          = {64}
}

@Article{Trebicka2017-lx,
  Author          = {Trebicka, Jonel},
  Title           = {Emergency {TIPS} in a {Child-Pugh} {B} patient: When
                    does the window of opportunity open and close?},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/j.jhep.2016.10.025},
  ids             = {trebicka_emergency_2017},
  Keywords        = {Trebicka-Selection},
  Number          = {2},
  Pages           = {442--450},
  Volume          = {66}
}

@Article{Trebicka2020-cy,
  Author          = {Trebicka, Jonel and Fernandez, Javier and Papp, Maria
                    and Caraceni, Paolo and Laleman, Wim and Gambino, Carmine
                    and Giovo, Ilaria and Uschner, Frank Erhard and Jimenez,
                    Cesar and Mookerjee, Rajeshwar and Gustot, Thierry and
                    Albillos, Agustin and Bañares, Rafael and Janicko,
                    Martin and Steib, Christian and Reiberger, Thomas and
                    Acevedo, Juan and Gatti, Pietro and Bernal, William and
                    Zeuzem, Stefan and Zipprich, Alexander and Piano,
                    Salvatore and Berg, Thomas and Bruns, Tony and Bendtsen,
                    Flemming and Coenraad, Minneke and Merli, Manuela and
                    Stauber, Rudolf and Zoller, Heinz and Ramos, José Presa
                    and Solè, Cristina and Soriano, Germán and de Gottardi,
                    Andrea and Gronbaek, Henning and Saliba, Faouzi and
                    Trautwein, Christian and Özdogan, Osman Cavit and
                    Francque, Sven and Ryder, Stephen and Nahon, Pierre and
                    Romero-Gomez, Manuel and Van Vlierberghe, Hans and
                    Francoz, Claire and Manns, Michael and Garcia, Elisabet
                    and Tufoni, Manuel and Amoros, Alex and Pavesi, Marco and
                    Sanchez, Cristina and Curto, Anna and Pitarch, Carla and
                    Putignano, Antonella and Moreno, Esau and Shawcross,
                    Debbie and Aguilar, Ferran and Clària, Joan and Ponzo,
                    Paola and Jansen, Christian and Vitalis, Zsuzsanna and
                    Zaccherini, Giacomo and Balogh, Boglarka and Vargas,
                    Victor and Montagnese, Sara and Alessandria, Carlo and
                    Bernardi, Mauro and Ginès, Pere and Jalan, Rajiv and
                    Moreau, Richard and Angeli, Paolo and Arroyo, Vicente and
                    {PREDICT STUDY group of the EASL-CLIF Consortium}},
  Title           = {The {PREDICT} study uncovers three clinical courses of
                    acutely decompensated cirrhosis that have distinct
                    pathophysiology},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jhep.2020.06.013},
  ids             = {trebicka_predict_2020},
  Keywords        = {Trebicka-Selection},
  Number          = {4},
  Pages           = {842--854},
  Volume          = {73}
}

@Article{Trebicka2021-jn,
  Author          = {Trebicka, Jonel and Fernandez, Javier and Papp, Maria
                    and Caraceni, Paolo and Laleman, Wim and Gambino, Carmine
                    and Giovo, Ilaria and Uschner, Frank Erhard and Jansen,
                    Christian and Jimenez, Cesar and Mookerjee, Rajeshwar and
                    Gustot, Thierry and Albillos, Agustin and Bañares,
                    Rafael and Jarcuska, Peter and Steib, Christian and
                    Reiberger, Thomas and Acevedo, Juan and Gatti, Pietro and
                    Shawcross, Debbie L and Zeuzem, Stefan and Zipprich,
                    Alexander and Piano, Salvatore and Berg, Thomas and
                    Bruns, Tony and Danielsen, Karen Vagner and Coenraad,
                    Minneke and Merli, Manuela and Stauber, Rudolf and
                    Zoller, Heinz and Ramos, José Presa and Solé, Cristina
                    and Soriano, Germán and de Gottardi, Andrea and
                    Gronbaek, Henning and Saliba, Faouzi and Trautwein,
                    Christian and Kani, Haluk Tarik and Francque, Sven and
                    Ryder, Stephen and Nahon, Pierre and Romero-Gomez, Manuel
                    and Van Vlierberghe, Hans and Francoz, Claire and Manns,
                    Michael and Garcia-Lopez, Elisabet and Tufoni, Manuel and
                    Amoros, Alex and Pavesi, Marco and Sanchez, Cristina and
                    Praktiknjo, Michael and Curto, Anna and Pitarch, Carla
                    and Putignano, Antonella and Moreno, Esau and Bernal,
                    William and Aguilar, Ferran and Clària, Joan and Ponzo,
                    Paola and Vitalis, Zsuzsanna and Zaccherini, Giacomo and
                    Balogh, Boglarka and Gerbes, Alexander and Vargas, Victor
                    and Alessandria, Carlo and Bernardi, Mauro and Ginès,
                    Pere and Moreau, Richard and Angeli, Paolo and Jalan,
                    Rajiv and Arroyo, Vicente and {PREDICT STUDY group of the
                    EASL-CLIF CONSORTIUM}},
  Title           = {{PREDICT} identifies precipitating events associated
                    with the clinical course of acutely decompensated
                    cirrhosis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jhep.2020.11.019},
  ids             = {trebicka_predict_2021},
  Keywords        = {Trebicka-Selection},
  Number          = {5},
  Pages           = {1097--1108},
  Volume          = {74}
}

@Article{Trebicka:834278,
  Author          = {Trebicka, Jonel and Macnaughtan, Jane and Schnabl, Bernd
                    and Shawcross, Debbie L. and Bajaj, Jasmohan S.},
  Title           = {The microbiota in cirrhosis and its role in hepatic
                    decompensation},
  JournalTitle    = {J. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jhep.2020.11.013},
  Keywords        = {Trebicka-Selection,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {Supplement 1},
  Pages           = {S67--S81},
  Volume          = {75}
}

@Article{Trebicka:834279,
  Author          = {Trebicka, Jonel and Bork, Peer and Krag, Aleksander and
                    Arumugam, Manimozhiyan},
  Title           = {Utilizing the gut microbiome in decompensated cirrhosis
                    and acute-on-chronic liver failure},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1038/s41575-020-00376-3},
  Keywords        = {Trebicka-Selection,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {3},
  Pages           = {167--180},
  Volume          = {18}
}

@Article{Tripathi2018-em,
  Author          = {Tripathi, Anupriya and Debelius, Justine and Brenner,
                    David A. and Karin, Michael and Loomba, Rohit and
                    Schnabl, Bernd and Knight, Rob},
  Title           = {The gut–liver axis and the intersection with the
                    microbiome},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2018},
  DOI             = {10.1038/s41575-018-0011-z},
  Number          = {7},
  Pages           = {397--411},
  Volume          = {15}
}

@Article{Trivedi2014,
  Author          = {Trivedi, Palak J. and Bruns, Tony and Cheung, Angela and
                    Li, Ka-Kit and Kittler, Clemens and Kumagi, Teru and
                    Shah, Husnain and Corbett, Christopher and Al-Harthy,
                    Nadya and Acarsu, Unsal and Coltescu, Catalina and
                    Tripathi, Dhiraj and Stallmach, Andreas and Neuberger,
                    James and Janssen, Harry L.A. and Hirschfield, Gideon
                    M.},
  Title           = {Optimising risk stratification in primary biliary
                    cirrhosis: {Ast/platelet} ratio index predicts outcome
                    independent of ursodeoxycholic acid response},
  JournalTitle    = {J. Hepatol.},
  Date            = {2014},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1016/j.jhep.2014.01.029},
  Addendum        = equal,
  Keywords        = {Bruns-Selection},
  Number          = {6},
  Pages           = {1249--1258},
  Volume          = {60}
}

@Article{Trivedi2016-rf,
  Author          = {Trivedi, Palak J and Bruns, Tony and Ward, Stephen and
                    Mai, Martina and Schmidt, Carsten and Hirschfield, Gideon
                    M and Weston, Chris J and Adams, David H},
  Title           = {Intestinal {CCL25} expression is increased in colitis
                    and correlates with inflammatory activity},
  JournalTitle    = {J. Autoimmun.},
  Date            = {2016},
  DOI             = {10.1016/j.jaut.2016.01.001},
  Pages           = {98--104},
  Volume          = {68}
}

@Article{Tschuor2016-js,
  Author          = {Tschuor, Christoph and Kachaylo, Ekaterina and Limani,
                    Përparim and Raptis, Dimitri A. and Linecker, Michael
                    and Tian, Yinghua and Herrmann, Uli and Grabliauskaite,
                    Kamile and Weber, Achim and Columbano, Amedeo and Graf,
                    Rolf and Humar, Bostjan and Clavien, Pierre-Alain},
  Title           = {Constitutive androstane receptor {(Car)}-driven
                    regeneration protects liver from failure following tissue
                    loss},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2016.02.040},
  Number          = {1},
  Pages           = {66--74},
  Volume          = {65}
}

@Article{Taute2015,
  Author          = {Taute, K.M. and Gude, S. and Tans, S.J. and Shimizu,
                    T.S.},
  Title           = {High-throughput {3D} tracking of bacteria on a standard
                    phase contrast microscope},
  JournalTitle    = {Nat. Commun.},
  Date            = {2015},
  DOI             = {10.1038/ncomms9776},
  Number          = {1},
  Volume          = {6}
}

@Article{Tsou2007-gn,
  Author          = {Tsou, Chia-Lin and Peters, Wendy and Si, Yue and
                    Slaymaker, Sarah and Aslanian, Ara M and Weisberg, Stuart
                    P and Mack, Matthias and Charo, Israel F},
  Title           = {Critical roles for {CCR2} and {MCP-3} in monocyte
                    mobilization from bone marrow and recruitment to
                    inflammatory sites},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2007},
  DOI             = {10.1172/JCI29919},
  Number          = {4},
  Pages           = {902--909},
  Volume          = {117}
}

@Article{Tsvetkova:717049,
  Author          = {Tsvetkova, Yoanna and Beztsinna, Nataliia and Baues,
                    Maike and Klein, Dionne and Rix, Anne and Golombek,
                    Susanne K. and Al Rawashdeh, Wa’el and Gremse, Felix
                    and Barz, Matthias and Koynov, Kaloian and Banala,
                    Srinivas and Lederle, Wiltrud and Lammers, Twan and
                    Kiessling, Fabian},
  Title           = {Balancing Passive and Active Targeting to Different
                    Tumor Compartments Using Riboflavin-Functionalized
                    Polymeric Nanocarriers},
  JournalTitle    = {Nano Lett.},
  Date            = {2017},
  DOI             = {10.1021/acs.nanolett.7b01171},
  Keywords        = {Kießling-Selection},
  Number          = {8},
  Pages           = {4665--4674},
  Volume          = {17}
}

@Article{Turkowsky2019-ys,
  Author          = {Türkowsky, Dominique and Lohmann, Patrick and
                    Mühlenbrink, Marie and Schubert, Torsten and Adrian,
                    Lorenz and Goris, Tobias and Jehmlich, Nico and von
                    Bergen, Martin},
  Title           = {Thermal proteome profiling allows quantitative
                    assessment of interactions between tetrachloroethene
                    reductive dehalogenase and trichloroethene},
  JournalTitle    = {J. Proteomics},
  Date            = {2019},
  DOI             = {10.1016/j.jprot.2018.05.018},
  Keywords        = {Dehalococcoides mccartyi; Organohalide respiration; PCE;
                    Proteome interaction; Quantitative proteomics; TCE},
  Pages           = {10--17},
  Volume          = {192}
}

@Article{Ubachs2021-bm,
  Author          = {Ubachs, Jorne and Ziemons, Janine and Soons, Zita and
                    Aarnoutse, Romy and Dijk, David P.J. and Penders, John
                    and Helvoort, Ardy and Smidt, Marjolein L. and
                    Kruitwagen, Roy F.P.M. and Baade‐Corpelijn, Lieke and
                    Olde Damink, Steven W.M. and Rensen, Sander S.},
  Title           = {Gut microbiota and short‐chain fatty acid alterations
                    in cachectic cancer patients},
  JournalTitle    = {J. Cachexia Sarcopenia Muscle},
  Date            = {2021},
  DOI             = {10.1002/jcsm.12804},
  Keywords        = {Olde Damink-Selection},
  Number          = {6},
  Pages           = {2007--2021},
  Volume          = {12}
}

@Article{Ugur:464883,
  Author          = {Ugur, Milas and Schulz, Olga and Menon, Manoj B. and
                    Krueger, Andreas and Pabst, Oliver},
  Title           = {Resident {CD4+} T cells accumulate in lymphoid organs
                    after prolonged antigen exposure},
  JournalTitle    = {Nat. Commun.},
  Date            = {2014},
  DOI             = {10.1038/ncomms5821},
  Keywords        = {Pabst-Selection,Peer-B06},
  Number          = {1},
  Pages           = {4821},
  Volume          = {5}
}

@Article{Ugur:757724,
  Author          = {Ugur, Milas and Kaminski, Anne and Pabst, Oliver},
  Title           = {Lymph node γδ and αβ {CD8+} T cells share migratory
                    properties},
  JournalTitle    = {Sci. Rep.},
  Date            = {2018},
  DOI             = {10.1038/s41598-018-27339-8},
  Keywords        = {Pabst-Selection},
  Number          = {1},
  Pages           = {8986},
  Volume          = {8}
}

@Article{Ullmann2021-el,
  Author          = {Ullmann, Lena and Phan, An N T and Kaplan, Daniel K P
                    and Blank, Lars M.},
  Title           = {Ustilaginaceae biocatalyst for co-metabolism of
                    {CO2-derived} substrates toward carbon-neutral itaconate
                    production},
  JournalTitle    = {J. Fungi (Basel)},
  Date            = {2021},
  DOI             = {10.3390/jof7020098},
  Keywords        = {CO2; Ustilaginaceae; Ustilago maydis; biodiversity;
                    chassis; itaconate; organic acid; smut fungi},
  Number          = {2},
  Pages           = {98},
  Volume          = {7}
}

@Article{Woitok2020-an,
  Author          = {Woitok, Marius Maximilian and Zoubek, Miguel Eugenio and
                    Doleschel, Dennis and Bartneck, Matthias and Mohamed,
                    Mohamed Ramadan and Kießling, Fabian and Lederle,
                    Wiltrud and Trautwein, Christian and Cubero, Francisco
                    Javier},
  Title           = {Lipid-encapsulated {siRNA} for hepatocyte-directed
                    treatment of advanced liver disease},
  JournalTitle    = {Cell Death Dis.},
  Date            = {2020},
  DOI             = {10.1038/s41419-020-2571-4},
  Number          = {5},
  Pages           = {343},
  Volume          = {11}
}

@Article{Ulmer:684984,
  Author          = {Ulmer, T. F. and de Jong, C. and Andert, A. and Bruners,
                    P. and Heidenhain, C. M. and Schoening, W. and Schmeding,
                    M. and Neumann, U. P.},
  Title           = {{ALPPS} Procedure in Insufficient Hypertrophy After
                    Portal Vein Embolization {(PVE)}},
  JournalTitle    = {World J. Surg.},
  Date            = {2016},
  DOI             = {10.1007/s00268-016-3662-3},
  ids             = {unknown-n},
  Number          = {1},
  Pages           = {250--257},
  Volume          = {41}
}

@Article{Ursell2012-pi,
  Author          = {Ursell, Luke K and Metcalf, Jessica L and Parfrey, Laura
                    Wegener and Knight, Rob},
  Title           = {Defining the human microbiome},
  JournalTitle    = {Nutr. Rev.},
  Date            = {2012},
  DOI             = {10.1111/j.1753-4887.2012.00493.x},
  Pages           = {S38--S44},
  Volume          = {70}
}

@Article{Van_Dijk2021-ad,
  Author          = {Dijk, David P.J. and Zhao, Junfang and Kemter, Katrin
                    and Baracos, Vickie E. and Dejong, Cornelis H.C. and
                    Rensen, Sander S. and Olde Damink, Steven W.M.},
  Title           = {Ectopic fat in liver and skeletal muscle is associated
                    with shorter overall survival in patients with colorectal
                    liver metastases},
  JournalTitle    = {J. Cachexia Sarcopenia Muscle},
  Date            = {2021},
  DOI             = {10.1002/jcsm.12723},
  Keywords        = {Olde Damink-Selection},
  Number          = {4},
  Pages           = {983--992},
  Volume          = {12}
}

@Article{Van_Golen2018-ws,
  Author          = {van Golen, Rowan F. and Olthof, Pim B. and Lionarons,
                    Daniël A. and Reiniers, Megan J. and Alles, Lindy K. and
                    Uz, Zehra and de Haan, Lianne and Ergin, Bulent and de
                    Waart, Dirk R. and Maas, Adrie and Verheij, Joanne and
                    Jansen, Peter L. and Damink, Steven W. Olde and Schaap,
                    Frank G. and van Gulik, Thomas M. and Heger, Michal},
  Title           = {{FXR} agonist obeticholic acid induces liver growth but
                    exacerbates biliary injury in rats with obstructive
                    cholestasis},
  JournalTitle    = {Sci. Rep.},
  Date            = {2018},
  DOI             = {10.1038/s41598-018-33070-1},
  Number          = {1},
  Pages           = {16529},
  Volume          = {8}
}

@Article{Van_de_Laarschot2016-ht,
  Author          = {van de Laarschot, Liyanne F. M. and Jansen, Peter L. M.
                    and Schaap, Frank G. and Olde Damink, Steven W. M.},
  Title           = {The role of bile salts in liver regeneration},
  JournalTitle    = {Hepatol. Int.},
  Date            = {2016},
  DOI             = {10.1007/s12072-016-9723-8},
  Number          = {5},
  Pages           = {733--740},
  Volume          = {10}
}

@Article{Vatanen2016-vk,
  Author          = {Vatanen, Tommi and Kostic, Aleksandar D. and
                    d’Hennezel, Eva and Siljander, Heli and Franzosa, Eric
                    A. and Yassour, Moran and Kolde, Raivo and Vlamakis, Hera
                    and Arthur, Timothy D. and Hämäläinen, Anu-Maaria and
                    Peet, Aleksandr and Tillmann, Vallo and Uibo, Raivo and
                    Mokurov, Sergei and Dorshakova, Natalya and Ilonen, Jorma
                    and Virtanen, Suvi M. and Szabo, Susanne J. and Porter,
                    Jeffrey A. and Lähdesmäki, Harri and Huttenhower,
                    Curtis and Gevers, Dirk and Cullen, Thomas W. and Knip,
                    Mikael and Xavier, Ramnik J.},
  Title           = {Variation in Microbiome {LPS} Immunogenicity Contributes
                    to Autoimmunity in Humans},
  JournalTitle    = {Cell},
  Date            = {2016},
  DOI             = {10.1016/j.cell.2016.04.007},
  Number          = {4},
  Pages           = {842--853},
  Volume          = {165}
}

@Article{Veenbergen:571107,
  Author          = {Veenbergen, S and van Berkel, L A and du Pré, M F and
                    He, J and Karrich, J J and Costes, L M M and Luk, F and
                    Simons-Oosterhuis, Y and Raatgeep, H C and Cerovic, V and
                    Cupedo, T and Mowat, A M and Kelsall, B L and Samsom, J
                    N},
  Title           = {Colonic tolerance develops in the iliac lymph nodes and
                    can be established independent of {CD103+} dendritic
                    cells},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2015},
  DOI             = {10.1038/mi.2015.118},
  Keywords        = {Cerovic-Selection},
  Number          = {4},
  Pages           = {894--906},
  Volume          = {9}
}

@Article{Verdeguer:685030,
  Author          = {Verdeguer, Francisco and Soustek, Meghan S. and Hatting,
                    Maximilian and Blättler, Sharon M. and McDonald, Devin
                    and Barrow, Joeva J. and Puigserver, Pere},
  Title           = {Brown Adipose {YY1} Deficiency Activates Expression of
                    Secreted Proteins Linked to Energy Expenditure and
                    Prevents Diet-Induced Obesity},
  JournalTitle    = {Mol. Cell. Biol.},
  Date            = {2016},
  DOI             = {10.1128/mcb.00722-15},
  Keywords        = {Hatting-Selection},
  Number          = {1},
  Pages           = {184--196},
  ShortJournal    = {MCB},
  Volume          = {36}
}

@Article{Verhaar2020-xw,
  Author          = {Verhaar, Barbara J. H. and Prodan, Andrei and Nieuwdorp,
                    Max and Muller, Majon},
  Title           = {Gut Microbiota in Hypertension and Atherosclerosis: {A}
                    Review},
  JournalTitle    = {Nutrients},
  Date            = {2020},
  DOI             = {10.3390/nu12102982},
  Number          = {10},
  Pages           = {2982},
  Volume          = {12}
}

@Article{Verjans:233347,
  Author          = {Verjans, Eva and Ohl, Kim and Yu, Yin and Lippe, Ralph
                    and Schippers, Angela and Wiener, Anastasia and Roth,
                    Johannes and Wagner, Norbert and Uhlig, Stefan and
                    Tenbrock, Klaus and Martin, Christian},
  Title           = {Overexpression of {CREMα} in T Cells Aggravates
                    Lipopolysaccharide-Induced Acute Lung Injury},
  JournalTitle    = {J. Immunol.},
  Date            = {2013},
  DOI             = {10.4049/jimmunol.1203147},
  Number          = {3},
  Pages           = {1316--1323},
  Volume          = {191}
}

@Article{Vickers2010-rw,
  Author          = {Vickers, Claudia E and Blank, Lars M. and Krömer, Jens
                    O},
  Title           = {Grand challenge commentary: Chassis cells for industrial
                    biochemical production},
  JournalTitle    = {Nat. Chem. Biol.},
  Date            = {2010},
  DOI             = {10.1038/nchembio.484},
  Addendum        = preliminarywork,
  Number          = {12},
  Pages           = {875--877},
  Volume          = {6}
}

@Article{Vogel2017-ox,
  Author          = {Vogel, Ida and Ott, Peter and Lildballe, Dorte and
                    Hamilton-Dutoit, Stephen and Vilstrup, Hendrik and
                    Gr{ø}nb{æ}k, Henning},
  Title           = {Isolated congenital hepatic fibrosis associated with
                    {TMEM67} mutations: report of a new genotype-phenotype
                    relationship},
  JournalTitle    = {Clin. Case Rep.},
  Date            = {2017},
  DOI             = {10.1002/ccr3.981},
  Keywords        = {Ciliopathy; TMEM67; congenital hepatic fibrosis;
                    meckelin},
  Number          = {7},
  Pages           = {1098--1102},
  Volume          = {5}
}

@Article{Vogel:460578,
  Author          = {Vogel, Arndt and Wege, Henning and Caca, Karel and
                    Nashan, Björn and Neumann, Ulf},
  Title           = {The Diagnosis and Treatment of Cholangiocarcinoma},
  JournalTitle    = {Deutsches Ärzteblatt international},
  Date            = {2014},
  DOI             = {10.3238/arztebl.2014.0748},
  Number          = {44},
  Pages           = {748--754},
  Volume          = {111}
}

@Article{Voronova2020-gi,
  Author          = {Voronova, Veronika and Sokolov, Victor and Al-Khaifi,
                    Amani and Straniero, Sara and Kumar, Chanchal and Peskov,
                    Kirill and Helmlinger, Gabriel and Rudling, Mats and
                    Angelin, Bo},
  Title           = {A Physiology-Based Model of Bile Acid Distribution and
                    Metabolism Under Healthy and Pathologic Conditions in
                    Human Beings},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jcmgh.2020.02.005},
  Keywords        = {Bile Acids; Cholesterol 7α-Hydroxylase; Farnesoid X
                    Receptor; Fibroblast Growth Factor-19; Physiology-Based
                    Modeling},
  Number          = {1},
  Pages           = {149--170},
  Volume          = {10}
}

@Article{Voss:834553,
  Author          = {Voss, Jessica and Schneider, Carolin Victoria and
                    Kleinjans, Moritz and Bruns, Tony and Trautwein,
                    Christian and Strnad, Pavel},
  Title           = {Hepatobiliary phenotype of individuals with chronic
                    intestinal disorders},
  JournalTitle    = {Sci. Rep.},
  Date            = {2021},
  DOI             = {10.1038/s41598-021-98843-7},
  Keywords        = {,CRC1382-Project B07,CRC1382-Project A03,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {19954},
  Volume          = {11}
}

@Article{Vucur:236060,
  Author          = {Vucur, Mihael and Reisinger, Florian and Gautheron,
                    Jérémie and Janssen, Joern and Roderburg, Christoph and
                    Cardenas, David Vargas and Kreggenwinkel, Karina and
                    Koppe, Christiane and Hammerich, Linda and Hakem, Razq
                    and Unger, Kristian and Weber, Achim and Gassler,
                    Nikolaus and Luedde, Mark and Frey, Norbert and Neumann,
                    Ulf Peter and Tacke, Frank and Trautwein, Christian and
                    Heikenwalder, Mathias and Luedde, Tom},
  Title           = {{RIP3} Inhibits Inflammatory Hepatocarcinogenesis but
                    Promotes Cholestasis by Controlling Caspase-8- and
                    {JNK}-Dependent Compensatory Cell Proliferation},
  JournalTitle    = {Cell Rep.},
  Date            = {2013},
  DOI             = {10.1016/j.celrep.2013.07.035},
  ids             = {vucur2013a},
  Keywords        = {Lüdde-Selection},
  Number          = {4},
  Pages           = {776--790},
  Volume          = {4}
}

@Article{WASNER200366,
  Author          = {Wasner, Mark and Tschöp, Katrin and Spiesbach, Katja
                    and Haugwitz, Ulrike and Johne, Cindy and Mössner,
                    Joachim and Mantovani, Roberto and Engeland, Kurt},
  Title           = {\emph{Cyclin B1} transcription is enhanced by the p300
                    coactivator and regulated during the cell cycle by a
                    {CHR}-dependent repression mechanism},
  JournalTitle    = {FEBS Lett.},
  Date            = {2003},
  DOI             = {10.1016/s0014-5793(03)00028-0},
  Number          = {1-3},
  Pages           = {66--70},
  Volume          = {536}
}

@Article{Wagner1996,
  Author          = {Wagner, Norbert and Löhler, Jürgen and Kunkel, Eric J.
                    and Ley, Klaus and Leung, Euphemia and Krissansen, Geoff
                    and Rajewsky, Klaus and Müller, Werner},
  Title           = {Critical role for β7 integrins in formation of the
                    gut-associated lymphoid tissue},
  JournalTitle    = {Nature},
  Date            = {1996},
  DOI             = {10.1038/382366a0},
  ids             = {wagner1996a},
  Keywords        = {Wagner-Selection},
  Number          = {6589},
  Pages           = {366--370},
  Volume          = {382}
}

@Article{Wagner:828378,
  Author          = {Wagner, Camille and Torow, Natalia and Hornef, Mathias
                    W. and Lelouard, Hugues},
  Title           = {Spatial and temporal key steps in early-life intestinal
                    immune system development and education},
  JournalTitle    = {FEBS J.},
  Date            = {2021},
  DOI             = {10.1111/febs.16047},
  ids             = {Wagner2022-hz},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)}
}

@Article{Wang2014-jg,
  Author          = {Wang, Rosy and Leong, Rupert W},
  Title           = {Primary sclerosing cholangitis as an independent risk
                    factor for colorectal cancer in the context of
                    inflammatory bowel disease: a review of the literature},
  JournalTitle    = {World J. Gastroenterol.},
  Date            = {2014},
  DOI             = {10.3748/wjg.v20.i27.8783},
  Keywords        = {Colorectal cancer; Crohn's; Inflammatory bowel disease;
                    Liver transplantation; Primary sclerosing cholangitis;
                    Ulcerative colitis; Ursodeoxycholic acid},
  Number          = {27},
  Pages           = {8783--8789},
  Volume          = {20}
}

@Article{Wang2014-uk,
  Author          = {Wang, Tiantian and Sun, Hui and Zhang, Jie and Liu, Qing
                    and Wang, Longjiang and Chen, Peipei and Wang, Fangkun
                    and Li, Hongmei and Xiao, Yihong and Zhao, Xiaomin},
  Title           = {The establishment of Saccharomyces boulardii surface
                    display system using a single expression vector},
  JournalTitle    = {Fungal Genet. Biol.},
  Date            = {2014},
  DOI             = {10.1016/j.fgb.2013.11.006},
  Keywords        = {EGFP; EtMic2p; S. boulardii; Surface display;
                    a-Agglutinin},
  Pages           = {1--10},
  Volume          = {64}
}

@Article{Wang2015,
  Author          = {Wang, Penghua and Zhu, Shu and Yang, Long and Cui,
                    Shuang and Pan, Wen and Jackson, Ruaidhri and Zheng,
                    Yunjiang and Rongvaux, Anthony and Sun, Qiangming and
                    Yang, Guang and Gao, Shandian and Lin, Rongtuan and You,
                    Fuping and Flavell, Richard and Fikrig, Erol},
  Title           = {Nlrp6 regulates intestinal antiviral innate immunity},
  JournalTitle    = {Science},
  DOI             = {10.1126/science.aab3145},
  Note            = {PMC4927078},
  Number          = {6262},
  Pages           = {826--830},
  Volume          = {350}
}

@Article{Weber:192210,
  Author          = {Weber, Christian and Noels, Heidi},
  Title           = {Atherosclerosis: {Current} pathogenesis and therapeutic
                    options},
  JournalTitle    = {Nat. Med.},
  Date            = {2011},
  DOI             = {10.1038/nm.2538},
  Number          = {11},
  Pages           = {1410--1422},
  Volume          = {17}
}

@Article{Weis2021Microbiota,
  Author          = {Weis, Allison M. and Round, June L.},
  Title           = {Microbiota-antibody interactions that regulate gut
                    homeostasis},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2021-03},
  DOI             = {10.1016/j.chom.2021.02.009},
  Number          = {3},
  Pages           = {334--346},
  Volume          = {29}
}

@Article{Weisberg2006-tv,
  Author          = {Weisberg, Stuart P and Hunter, Deborah and Huber, Reid
                    and Lemieux, Jacob and Slaymaker, Sarah and Vaddi, Kris
                    and Charo, Israel and Leibel, Rudolph L and Ferrante, Jr,
                    Anthony W},
  Title           = {{CCR2} modulates inflammatory and metabolic effects of
                    high-fat feeding},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2006},
  DOI             = {10.1172/JCI24335},
  Number          = {1},
  Pages           = {115--124},
  Volume          = {116}
}

@Article{Wen:815760,
  Author          = {Wen, Yankai and Lambrecht, Joeri and Ju, Cynthia and
                    Tacke, Frank},
  Title           = {Hepatic macrophages in liver homeostasis and
                    diseases-diversity, plasticity and therapeutic
                    opportunities},
  JournalTitle    = {Cell. Mol. Immunol.},
  Date            = {2021},
  DOI             = {10.1038/s41423-020-00558-8},
  Keywords        = {,CRC1382-Project B05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {45--56},
  Volume          = {18}
}

@Article{Westrom2020-pj,
  Author          = {Weström, Björn and Arévalo Sureda, Ester and
                    Pierzynowska, Kateryna and Pierzynowski, Stefan G. and
                    Pérez-Cano, Francisco-José},
  Title           = {The Immature Gut Barrier and Its Importance in
                    Establishing Immunity in Newborn Mammals},
  JournalTitle    = {Front. Immunol.},
  Date            = {2020},
  DOI             = {10.3389/fimmu.2020.01153},
  Keywords        = {FcRn; fetal; immunity; intestine; permeability;
                    tolerance; transcytosis},
  Pages           = {1153},
  Volume          = {11}
}

@Article{Wiest2005Bacterial,
  Author          = {Wiest, Reiner and Garcia-Tsao, Guadalupe},
  Title           = {Bacterial translocation {(BT)} in cirrhosis},
  JournalTitle    = {Hepatology},
  Date            = {2005-03},
  DOI             = {10.1002/hep.20632},
  Number          = {3},
  Pages           = {422--433},
  Volume          = {41}
}

@Article{Wirtz2019-ek,
  Author          = {Wirtz, Theresa Hildegard and Brandt, Elisa Fabiana and
                    Berres, Marie-Luise},
  Title           = {Liver {DCs} in health and disease},
  JournalTitle    = {Int. Rev. Cell Mol. Biol.},
  Date            = {2019},
  DOI             = {10.1016/bs.ircmb.2019.08.001},
  Pages           = {263--299},
  Volume          = {348}
}

@Article{Wirtz:803971,
  Author          = {Wirtz, Theresa H. and Loosen, Sven H. and Buendgens,
                    Lukas and Kurt, Berkan and Abu Jhaisha, Samira and
                    Hohlstein, Philipp and Brozat, Jonathan F. and
                    Weiskirchen, Ralf and Lüdde, Tom and Tacke, Frank and
                    Trautwein, Christian and Roderburg, Christoph and Koch,
                    Alexander},
  Title           = {Low Myostatin Serum Levels Are Associated with Poor
                    Outcome in Critically Ill Patients},
  JournalTitle    = {Diagnostics},
  Date            = {2020},
  DOI             = {10.3390/diagnostics10080574},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project B05,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {8},
  Volume          = {10}
}

@Article{Wirtz:811445,
  Author          = {Wirtz, Theresa H. and Reuken, Philipp A. and Jansen,
                    Christian and Fischer, Petra and Bergmann, Irina and
                    Backhaus, Christina and Emontzpohl, Christoph and
                    Reißing, Johanna and Brandt, Elisa Fabiana and Koenen,
                    M. Teresa and Schneider, Kai M. and Schierwagen, Robert
                    and Brol, Maximilian J. and Chang, Johannes and
                    Zimmermann, Henning W. and Köse-Vogel, Nilay and
                    Eggermann, Thomas and Kurth, Ingo and Stoppe, Christian
                    and Bucala, Richard and Bernhagen, Jürgen and
                    Praktiknjo, Michael and Stallmach, Andreas and Trautwein,
                    Christian and Trebicka, Jonel and Bruns, Tony and Berres,
                    Marie-Luise},
  Title           = {Balance between macrophage migration inhibitory factor
                    and s{CD}74 predicts outcome in patients with acute
                    decompensation of cirrhosis},
  JournalTitle    = {JHEP Reports},
  Date            = {2021},
  DOI             = {10.1016/j.jhepr.2020.100221},
  ids             = {Wirtz2021-ug},
  Keywords        = {Wirtz-Selection,Berres-Selection,CRC1382-Project
                    B04,CRC1382-Project B04,CRC1382-Project
                    B07,CRC1382-Project A09,CRC1382-Project
                    A06,CRC1382-Project A08,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {2},
  Pages           = {100221},
  Volume          = {3}
}

@Article{Wirtz:813391,
  Author          = {Wirtz, Theresa H. and Buendgens, Lukas and Weiskirchen,
                    Ralf and Loosen, Sven H. and Haehnsen, Nina and Puengel,
                    Tobias and Abu Jhaisha, Samira and Brozat, Jonathan F.
                    and Hohlstein, Philipp and Koek, Ger and Eisert, Albrecht
                    and Mohr, Raphael and Roderburg, Christoph and Lüdde,
                    Tom and Trautwein, Christian and Tacke, Frank and Koch,
                    Alexander},
  Title           = {Association of Serum Calprotectin Concentrations with
                    Mortality in Critically Ill and Septic Patients},
  JournalTitle    = {Diagnostics},
  Date            = {2020},
  DOI             = {10.3390/diagnostics10110990},
  Keywords        = {,CRC1382-Project A01,CRC1382-Project B05,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {11},
  Volume          = {10}
}

@Article{Wirtz:828618,
  Author          = {Wirtz, Theresa H. and Saal, Alena and Bergmann, Irina
                    and Fischer, Petra and Heinrichs, Daniel and Brandt,
                    Elisa Fabiana and Koenen, Maria Teresa and Djudjaj, Sonja
                    and Schneider, Kai Markus and Boor, Peter and Bucala,
                    Richard and Weiskirchen, Ralf and Bernhagen, Jürgen and
                    Trautwein, Christian and Berres, Marie-Luise},
  Title           = {Macrophage migration inhibitory factor exerts
                    pro‐proliferative and anti‐apoptotic effects via
                    {CD}74 in murine hepatocellular carcinoma},
  JournalTitle    = {Br. J. Pharmacol.},
  Date            = {2021},
  DOI             = {10.1111/bph.15622},
  ids             = {Wirtz2021-tn},
  Keywords        = {Wirtz-Selection,Berres-Selection,CRC1382-Project
                    B04,CRC1382-Project B04,CRC1382-Project
                    A06,CRC1382-Project A08},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {22},
  Pages           = {4452--4467},
  Volume          = {178}
}

@Article{Wissenbach2016,
  Author          = {Wissenbach, Dirk K. and Oliphant, Kaitlyn and
                    Rolle-Kampczyk, Ulrike and Yen, Sandi and Höke, Henrike
                    and Baumann, Sven and Haange, Sven B. and Verdu, Elena F.
                    and Allen-Vercoe, Emma and von Bergen, Martin},
  Title           = {Optimization of metabolomics of defined in vitro gut
                    microbial ecosystems},
  JournalTitle    = {Int. J. Med. Microbiol.},
  Date            = {2016},
  DOI             = {10.1016/j.ijmm.2016.03.007},
  ids             = {wissenschbach2016a},
  Keywords        = {von Bergen-Selection},
  Number          = {5},
  Pages           = {280--289},
  Volume          = {306}
}

@Article{Wit2022-qz,
  Author          = {Wit, Magdalena and Trujillo-Viera, Jonathan and
                    Strohmeyer, Akim and Klingenspor, Martin and Hankir,
                    Mohammed and Sumara, Grzegorz},
  Title           = {When fat meets the gut-focus on intestinal lipid
                    handling in metabolic health and disease},
  JournalTitle    = {EMBO Mol. Med.},
  Date            = {2022},
  DOI             = {10.15252/emmm.202114742},
  Keywords        = {enterocyte; fat absorption; intestine; metabolic
                    diseases; triglycerides},
  Number          = {5},
  Pages           = {e14742},
  Volume          = {14}
}

@Article{Woehlke1994-yb,
  Author          = {Woehlke, G and Dimroth, P},
  Title           = {Anaerobic growth of Salmonella typhimurium on L(+)- and
                    D(-)-tartrate involves an oxaloacetate decarboxylase Na+
                    pump},
  JournalTitle    = {Arch. Microbiol.},
  Date            = {1994},
  DOI             = {10.1007/BF00301843},
  Number          = {4},
  Pages           = {233--237},
  Volume          = {162}
}

@Book{Wu2022-if,
  Author          = {Wu, Zhuojun and Jankowski, Joachim},
  Title           = {Impact of post-translational modification on the genesis
                    and progression of diseases},
  JournalTitle    = {Mol. Asp. Med.},
  Date            = {2022},
  DOI             = {https://doi.org/10.1016/j.mam.2022.101105},
  Keywords        = {Jankowski-Selection},
  Note            = {Impact of Post-Translational Modification on the Genesis
                    and Progression of Diseases},
  Pages           = {101105},
  Volume          = {86}
}

@Article{Wuichet2010Origins,
  Author          = {Wuichet, Kristin and Zhulin, Igor B.},
  Title           = {Origins and Diversification of a Complex Signal
                    Transduction System in Prokaryotes},
  JournalTitle    = {Sci. Signal.},
  Date            = {2010-06-29},
  DOI             = {10.1126/scisignal.2000724},
  Note            = {[Online; accessed 2022-07-22]},
  Number          = {128},
  Volume          = {3}
}

@Article{Wylensek2020-jm,
  Author          = {Wylensek, David and Hitch, Thomas C A and Riedel, Thomas
                    and Afrizal, Afrizal and Kumar, Neeraj and Wortmann,
                    Esther and Liu, Tianzhe and Devendran, Saravanan and
                    Lesker, Till R and Hernández, Sara B and Heine, Viktoria
                    and Buhl, Eva M and M D'Agostino, Paul and Cumbo, Fabio
                    and Fischöder, Thomas and Wyschkon, Marzena and Looft,
                    Torey and Parreira, Valeria R and Abt, Birte and Doden,
                    Heidi L and Ly, Lindsey and Alves, João M P and
                    Reichlin, Markus and Flisikowski, Krzysztof and Suarez,
                    Laura Navarro and Neumann, Anthony P and Suen, Garret and
                    de Wouters, Tomas and Rohn, Sascha and Lagkouvardos,
                    Ilias and Allen-Vercoe, Emma and Spröer, Cathrin and
                    Bunk, Boyke and Taverne-Thiele, Anja J and Giesbers,
                    Marcel and Wells, Jerry M and Neuhaus, Klaus and
                    Schnieke, Angelika and Cava, Felipe and Segata, Nicola
                    and Elling, Lothar and Strowig, Till and Ridlon, Jason M
                    and Gulder, Tobias A M and Overmann, Jörg and Clavel,
                    Thomas},
  Title           = {A collection of bacterial isolates from the pig
                    intestine reveals functional and taxonomic diversity},
  JournalTitle    = {Nat. Commun.},
  Addendum        = preliminarywork,
  Date            = {2020},
  DOI             = {10.1038/s41467-020-19929-w},
  Keywords        = {Clavel-Selection},
  Number          = {1},
  Pages           = {6389},
  Volume          = {11}
}

@Article{Xiao2015Over-activation,
  Author          = {Xiao, Yang and Liu, Fang and Yang, Jingyi and Zhong,
                    Maohua and Zhang, Ejuan and Li, Yaoming and Zhou, Dihan
                    and Cao, Yuan and Li, Wei and Yu, Jie and Yang, Yi and
                    Yan, Huimin},
  Title           = {Over-activation of {TLR5} signaling by high-dose
                    flagellin induces liver injury in mice},
  JournalTitle    = {Cellular \& Molecular Immunology},
  Date            = {2015-11},
  DOI             = {10.1038/cmi.2014.110},
  Number          = {6},
  Pages           = {729--742},
  Volume          = {12}
}

@Article{Xie2011Bacterial,
  Author          = {Xie, Li and Altindal, Tuba and Chattopadhyay, Suddhashil
                    and Wu, Xiao-Lun},
  Title           = {Bacterial flagellum as a propeller and as a rudder for
                    efficient chemotaxis},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2011},
  DOI             = {10.1073/pnas.1011953108},
  Number          = {6},
  Pages           = {2246--2251},
  Volume          = {108}
}

@Article{Xue2018-kk,
  Author          = {Xue, Rufeng and Zhang, Huimin and Pan, Jun and Du,
                    Zhiwei and Zhou, Wenjie and Zhang, Zhi and Tian, Zhigang
                    and Zhou, Rongbin and Bai, Li},
  Title           = {Peripheral dopamine controlled by gut microbes inhibits
                    invariant natural killer {T} cell-mediated hepatitis},
  JournalTitle    = {Front. Immunol.},
  Date            = {2018},
  DOI             = {10.3389/fimmu.2018.02398},
  Keywords        = {D1-like receptors; dopamine; gut microbes; hepatitis;
                    iNKT},
  Pages           = {2398},
  Volume          = {9}
}

@Article{Yang2018-gx,
  Author          = {Yang, Ju and Yan, Jing and Liu, Baorui},
  Title           = {Targeting {VEGF/VEGFR} to Modulate Antitumor Immunity},
  JournalTitle    = {Front. Immunol.},
  Date            = {2018},
  DOI             = {10.3389/fimmu.2018.00978},
  Pages           = {978},
  Volume          = {9}
}

@Article{Yang2017TLR5,
  Author          = {Yang, Jingyi and Yan, Huimin},
  Title           = {{TLR5:} {Beyond} the recognition of flagellin},
  JournalTitle    = {Cellular \& Molecular Immunology},
  Date            = {2017-12},
  DOI             = {10.1038/cmi.2017.122},
  Number          = {12},
  Pages           = {1017--1019},
  Volume          = {14}
}

@Article{Yatsunenko2012-ib,
  Author          = {Yatsunenko, Tanya and Rey, Federico E. and Manary, Mark
                    J. and Trehan, Indi and Dominguez-Bello, Maria Gloria and
                    Contreras, Monica and Magris, Magda and Hidalgo, Glida
                    and Baldassano, Robert N. and Anokhin, Andrey P. and
                    Heath, Andrew C. and Warner, Barbara and Reeder, Jens and
                    Kuczynski, Justin and Caporaso, J. Gregory and Lozupone,
                    Catherine A. and Lauber, Christian and Clemente, Jose
                    Carlos and Knights, Dan and Knight, Rob and Gordon,
                    Jeffrey I.},
  Title           = {Human gut microbiome viewed across age and geography},
  JournalTitle    = {Nature},
  Date            = {2012},
  DOI             = {10.1038/nature11053},
  ids             = {yatsunenko2012a},
  Number          = {7402},
  Pages           = {222--227},
  Volume          = {486}
}

@Article{Yoon2018-op,
  Author          = {Yoon, Hongsup and Schaubeck, Monika and Lagkouvardos,
                    Ilias and Blesl, Andreas and Heinzlmeir, Stephanie and
                    Hahne, Hannes and Clavel, Thomas and Panda, Suchita and
                    Ludwig, Christina and Kuster, Bernhard and Manichanh,
                    Chaysavanh and Kump, Patrizia and Haller, Dirk and
                    Hörmannsperger, Gabriele},
  Title           = {Increased Pancreatic Protease Activity in Response to
                    Antibiotics Impairs Gut Barrier and Triggers Colitis},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/j.jcmgh.2018.05.008},
  Number          = {3},
  Pages           = {370--388.e3},
  Volume          = {6}
}

@Article{Spadoni2015,
  Author          = {Spadoni, Ilaria and Zagato, Elena and Bertocchi, Alice
                    and Paolinelli, Roberta and Hot, Edina and Di Sabatino,
                    Antonio and Caprioli, Flavio and Bottiglieri, Luca and
                    Oldani, Amanda and Viale, Giuseppe and Penna, Giuseppe
                    and Dejana, Elisabetta and Rescigno, Maria},
  Title           = {A gut-vascular barrier controls the systemic
                    dissemination of bacteria},
  JournalTitle    = {Science},
  Date            = {2015},
  DOI             = {10.1126/science.aad0135},
  Number          = {6262},
  Pages           = {830--834},
  Volume          = {350}
}

@Article{Kok2021,
  Author          = {Kok, Lianne and Masopust, David and Schumacher, Ton N.},
  Title           = {The precursors of {CD8+} tissue resident memory T cells:
                    {From} lymphoid organs to infected tissues},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2021},
  DOI             = {10.1038/s41577-021-00590-3},
  Number          = {5},
  Pages           = {283--293},
  Volume          = {22}
}

@Article{Farowski2019,
  Author          = {Farowski, Fedja and Solbach, Philipp and Tsakmaklis,
                    Anastasia and Brodesser, Susanne and Cruz Aguilar, M.
                    Rebeca and Cornely, Oliver A. and Dettmer, Katja and
                    Higgins, Paul G. and Suerbaum, Sebastian and Jazmati,
                    Nathalie and Oefner, Peter J. and Vehreschild, Maria
                    J.G.T.},
  Title           = {Potential biomarkers to predict outcome of faecal
                    microbiota transfer for recurrent Clostridioides
                    difficile infection},
  JournalTitle    = {Dig. Dis. Sci.},
  Date            = {2019},
  Addendum        = preliminarywork,
  DOI             = {10.1016/j.dld.2019.01.012},
  Number          = {7},
  Pages           = {944--951},
  Volume          = {51}
}

@Article{Younossi2021,
  Author          = {Younossi, Zobair M and Stepanova, Maria and Ong, Janus
                    and Trimble, Greg and AlQahtani, Saleh and Younossi,
                    Issah and Ahmed, Aijaz and Racila, Andrei and Henry,
                    Linda},
  Title           = {Nonalcoholic steatohepatitis is the most rapidly
                    increasing indication for liver transplantation in the
                    United States},
  JournalTitle    = {Clin. Gastroenterol. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.cgh.2020.05.064},
  Keywords        = {Etiology; Incidence; Liver cancer; Time periods},
  Number          = {3},
  Pages           = {580--589.e5},
  Volume          = {19}
}

@Article{Zambito2021-lx,
  Author          = {Zambito, Giorgia and Hall, Mary P. and Wood, Monika G.
                    and Gaspar, Natasa and Ridwan, Yanto and Stellari, Fabio
                    F. and Shi, Ce and Kirkland, Thomas A. and Encell, Lance
                    P. and Löwik, Clemens and Mezzanotte, Laura},
  Title           = {Red-shifted click beetle luciferase mutant expands the
                    multicolor bioluminescent palette for deep tissue
                    imaging},
  JournalTitle    = {iScience},
  Date            = {2021},
  DOI             = {10.1016/j.isci.2020.101986},
  Number          = {1},
  Pages           = {101986},
  Volume          = {24}
}

@Article{Zafarnia2019-oh,
  Author          = {Zafarnia, Sara and Mrugalla, Anna and Rix, Anne and
                    Doleschel, Dennis and Gremse, Felix and Wolf, Stephanie
                    D. and Buyel, Johannes F. and Albrecht, Ute and Bode,
                    Johannes G. and Kiessling, Fabian and Lederle, Wiltrud},
  Title           = {Non-invasive Imaging and Modeling of Liver Regeneration
                    After Partial Hepatectomy},
  JournalTitle    = {Front. Physiol.},
  Date            = {2019},
  DOI             = {10.3389/fphys.2019.00904},
  Keywords        = {Lederle-Selection},
  Pages           = {904},
  Volume          = {10}
}

@Article{Zafarnia:717051,
  Author          = {Zafarnia, Sara and Bzyl-Ibach, Jessica and Spivak, Igor
                    and Li, Yongping and Koletnik, Susanne and Doleschel,
                    Dennis and Rix, Anne and Pochon, Sibylle and Tardy,
                    Isabelle and Koyadan, Seena and van Zandvoort, Marc and
                    Palmowski, Moritz and Kiessling, Fabian and Lederle,
                    Wiltrud},
  Title           = {Nilotinib Enhances Tumor Angiogenesis and Counteracts
                    {VEGFR2} Blockade in an Orthotopic Breast Cancer
                    Xenograft Model with Desmoplastic Response},
  JournalTitle    = {Neoplasia},
  Date            = {2017},
  DOI             = {10.1016/j.neo.2017.08.009},
  Keywords        = {Lederle-Selection},
  Number          = {11},
  Pages           = {896--907},
  Volume          = {19}
}

@Article{Zantow2016,
  Author          = {Zantow, Jonas and Just, Sarah and Lagkouvardos, Ilias
                    and Kisling, Sigrid and Dübel, Stefan and Lepage,
                    Patricia and Clavel, Thomas and Hust, Michael},
  Title           = {Mining gut microbiome oligopeptides by functional
                    metaproteome display},
  JournalTitle    = {Sci. Rep.},
  Date            = {2016},
  DOI             = {10.1038/srep34337},
  Number          = {1},
  Volume          = {6}
}

@Article{Zarrinpar2018-os,
  Author          = {Zarrinpar, Amir and Chaix, Amandine and Xu, Zhenjiang Z.
                    and Chang, Max W. and Marotz, Clarisse A. and
                    Saghatelian, Alan and Knight, Rob and Panda,
                    Satchidananda},
  Title           = {Antibiotic-induced microbiome depletion alters metabolic
                    homeostasis by affecting gut signaling and colonic
                    metabolism},
  JournalTitle    = {Nat. Commun.},
  Date            = {2018},
  DOI             = {10.1038/s41467-018-05336-9},
  Number          = {1},
  Pages           = {2872},
  Volume          = {9}
}

@Article{Zeissig2019-vn,
  Author          = {Zeissig, Sebastian and Rosati, Elisa and Dowds, C Marie
                    and Aden, Konrad and Bethge, Johannes and Schulte,
                    Berenice and Pan, Wei Hung and Mishra, Neha and Zuhayra,
                    Maaz and Marx, Marlies and Paulsen, Maren and Strigli,
                    Anne and Conrad, Claudio and Schuldt, Dörthe and Sinha,
                    Anupam and Ebsen, Henriette and Kornell, Sabin-Christin
                    and Nikolaus, Susanna and Arlt, Alexander and Kabelitz,
                    Dieter and Ellrichmann, Mark and Lützen, Ulf and
                    Rosenstiel, Philip C and Franke, Andre and Schreiber,
                    Stefan},
  Title           = {Vedolizumab is associated with changes in innate rather
                    than adaptive immunity in patients with inflammatory
                    bowel disease},
  JournalTitle    = {Gut},
  Date            = {2019},
  DOI             = {10.1136/gutjnl-2018-316023},
  Keywords        = {crohn's disease; inflammatory bowel disease; integrins;
                    ulcerative colitis},
  Number          = {1},
  Pages           = {25--39},
  Volume          = {68}
}

@Article{ZengBrouwers:815763,
  Author          = {Zeng-Brouwers, Jinyang and Pandey, Sony and Trebicka,
                    Jonel and Wygrecka, Malgorzata and Schaefer, Liliana},
  Title           = {Communications via the Small Leucine-rich Proteoglycans:
                    Molecular Specificity in Inflammation and Autoimmune
                    Diseases},
  JournalTitle    = {J. Histochem. Cytochem.},
  Date            = {2020},
  DOI             = {10.1369/0022155420930303},
  Keywords        = {,CRC1382-Project A09},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {12},
  Pages           = {887--906},
  Volume          = {68}
}

@Article{Zenner2021-bx,
  Author          = {Zenner, Christian and Hitch, Thomas C. A. and Riedel,
                    Thomas and Wortmann, Esther and Tiede, Stefan and Buhl,
                    Eva M. and Abt, Birte and Neuhaus, Klaus and Velge,
                    Philippe and Overmann, Jörg and Kaspers, Bernd and
                    Clavel, Thomas},
  Title           = {Early-life immune system maturation in chickens using a
                    synthetic community of cultured gut bacteria},
  JournalTitle    = {mSystems},
  Date            = {2021},
  DOI             = {10.1128/mSystems.01300-20},
  Keywords        = {Clavel-Selection},
  Number          = {3},
  Volume          = {6}
}

@Article{Zhang2014-cf,
  Author          = {Zhang, Kaiyi and Dupont, Aline and Torow, Natalia and
                    Gohde, Fredrik and Leschner, Sara and Lienenklaus, Stefan
                    and Weiss, Siegfried and Brinkmann, Melanie M. and
                    Kühnel, Mark and Hensel, Michael and Fulde, Marcus and
                    Hornef, Mathias W.},
  Title           = {Age-Dependent Enterocyte Invasion and Microcolony
                    Formation by Salmonella},
  JournalTitle    = {PLoS Pathog.},
  Date            = {2014},
  DOI             = {10.1371/journal.ppat.1004385},
  Number          = {9},
  Pages           = {e1004385},
  Volume          = {10}
}

@Article{Zhang:756776,
  Author          = {Zhang, Kaiyi and Riba, Ambre and Nietschke, Monika and
                    Torow, Natalia and Repnik, Urska and Pütz, Andreas and
                    Fulde, Marcus and Dupont, Aline and Hensel, Michael and
                    Hornef, Mathias W.},
  Title           = {Minimal {SPI1}-{T3SS} effector requirement for
                    Salmonella enterocyte invasion and intracellular
                    proliferation in vivo},
  JournalTitle    = {PLoS Pathog.},
  Date            = {2018},
  DOI             = {10.1371/journal.ppat.1006925},
  Keywords        = {Hornef-Selection},
  Number          = {3},
  Pages           = {e1006925},
  Volume          = {14}
}

@Article{Zhao2011NLRC4,
  Author          = {Zhao, Yue and Yang, Jieling and Shi, Jianjin and Gong,
                    Yi-Nan and Lu, Qiuhe and Xu, Hao and Liu, Liping and
                    Shao, Feng},
  Title           = {The {NLRC4} inflammasome receptors for bacterial
                    flagellin and type {III} secretion apparatus},
  JournalTitle    = {Nature},
  Date            = {2011-09},
  DOI             = {10.1038/nature10510},
  Number          = {7366},
  Pages           = {596--600},
  Volume          = {477}
}

@Article{Zhao:446193,
  Author          = {Zhao, Gang and Hatting, Maximilian and Nevzorova, Yulia
                    A. and Peng, Jin and Hu, Wei and Boekschoten, Mark V and
                    Roskams, Tania and Muller, Michael and Gassler, Nikolaus
                    and Liedtke, Christian and Davis, Roger J and Cubero,
                    Francisco Javier and Trautwein, Christian},
  Title           = {Jnk1 in murine hepatic stellate cells is a crucial
                    mediator of liver fibrogenesis},
  JournalTitle    = {Gut},
  Date            = {2013},
  DOI             = {10.1136/gutjnl-2013-305507},
  Number          = {7},
  Pages           = {1159--1172},
  Volume          = {63}
}

@Article{Zheng2020-xi,
  Author          = {Zheng, Danping and Liwinski, Timur and Elinav, Eran},
  Title           = {Interaction between microbiota and immunity in health
                    and disease},
  JournalTitle    = {Cell Res.},
  Date            = {2020},
  DOI             = {10.1038/s41422-020-0332-7},
  Number          = {6},
  Pages           = {492--506},
  Volume          = {30}
}

@Article{Zhou2017-jz,
  Author          = {Zhou, Guoying and Sprengers, Dave and Boor, Patrick P.C.
                    and Doukas, Michail and Schutz, Hannah and Mancham,
                    Shanta and Pedroza-Gonzalez, Alexander and Polak,
                    Wojciech G. and de Jonge, Jeroen and Gaspersz, Marcia and
                    Dong, Haidong and Thielemans, Kris and Pan, Qiuwei and
                    IJzermans, Jan N.M. and Bruno, Marco J. and Kwekkeboom,
                    Jaap},
  Title           = {Antibodies Against Immune Checkpoint Molecules Restore
                    Functions of Tumor-Infiltrating T Cells in Hepatocellular
                    Carcinomas},
  JournalTitle    = {Gastroenterology},
  Date            = {2017},
  DOI             = {10.1053/j.gastro.2017.06.017},
  Number          = {4},
  Pages           = {1107--1119.e10},
  Volume          = {153}
}

@Article{Czigany2019,
  Author          = {Czigany, Zoltan and Kramp, Wiebke and Bednarsch, Jan and
                    Kroft, Gregory and Boecker, Joerg and Strnad, Pavel and
                    Zimmermann, Markus and Koek, Ger and Neumann, Ulf Peter
                    and Lurje, Georg},
  Title           = {Myosteatosis to predict inferior perioperative outcome
                    in patients undergoing orthotopic liver transplantation},
  JournalTitle    = {Am. J. Transplant.},
  Date            = {2019},
  Addendum        = preliminarywork,
  DOI             = {10.1111/ajt.15577},
  Number          = {2},
  Pages           = {493--503},
  Volume          = {20}
}

@Article{Czigany2021,
  Author          = {Czigany, Zoltan and Kramp, Wiebke and Lurje, Isabella
                    and Miller, Hannah and Bednarsch, Jan and Lang, Sven Arke
                    and Ulmer, Tom Florian and Bruners, Philipp and Strnad,
                    Pavel and Trautwein, Christian and Websky, Martin
                    Wolfgang and Tacke, Frank and Neumann, Ulf Peter and
                    Lurje, Georg},
  Title           = {The role of recipient myosteatosis in graft and patient
                    survival after deceased donor liver transplantation},
  JournalTitle    = {J. Cachexia Sarcopenia Muscle},
  Date            = {2021},
  DOI             = {10.1002/jcsm.12669},
  Number          = {2},
  Pages           = {358--367},
  Addendum        = preliminarywork,
  Volume          = {12}
}

@Article{Zimmermann2013,
  Author          = {Zimmermann, H. W. and Reuken, P. A. and Koch, A. and
                    Bartneck, M. and Adams, D. H. and Trautwein, C. and
                    Stallmach, A. and Tacke, F. and Bruns, T.},
  Title           = {Soluble urokinase plasminogen activator receptor is
                    compartmentally regulated in decompensated cirrhosis and
                    indicates immune activation and short-term mortality},
  JournalTitle    = {J. Intern. Med.},
  Date            = {2013},
  DOI             = {10.1111/joim.12054},
  Keywords        = {Bruns-Selection},
  Number          = {1},
  Pages           = {86--100},
  Volume          = {274}
}

@Article{Zimmermann2015,
  Author          = {Zimmermann, Henning W. and Bruns, Tony and Weston, Chris
                    J. and Curbishley, Stuart M. and Liaskou, Evaggelia and
                    Li, Ka-Kit and Resheq, Yazid J. and Badenhorst, Paul W.
                    and Adams, David H.},
  Title           = {Bidirectional transendothelial migration of monocytes
                    across hepatic sinusoidal endothelium shapes monocyte
                    differentiation and regulates the balance between
                    immunity and tolerance in liver},
  JournalTitle    = {Hepatology},
  Date            = {2015},
  DOI             = {10.1002/hep.28285},
  Number          = {1},
  Pages           = {233--246},
  Subtitle        = {Liver Biology/Pathobiology},
  Volume          = {63}
}

@Article{Zimmermann2021-zq,
  Author          = {Zimmermann, Johannes and Kaleta, Christoph and Waschina,
                    Silvio},
  Title           = {Gapseq: Informed prediction of bacterial metabolic
                    pathways and reconstruction of accurate metabolic
                    models},
  JournalTitle    = {Genome Biol.},
  Date            = {2021},
  DOI             = {10.1186/s13059-021-02295-1},
  Keywords        = {Benchmark; Community simulation; Genome-scale metabolic
                    models; Metabolic networks; Metabolic pathway analysis;
                    Metagenome; Microbiome},
  Number          = {1},
  Pages           = {81},
  Volume          = {22}
}

@Article{Gross2022-zo,
  Author          = {Gross, Annika and Zhou, Biaohuan and Bewersdorf, Lisa
                    and Schwarz, Nicole and Schacht, Gabriel M. and Boor,
                    Peter and Hoeft, Konrad and Hoffmann, Bernd and Fuchs,
                    Elaine and Kramann, Rafael and Merkel, Rudolf and Leube,
                    Rudolf E. and Strnad, Pavel},
  Title           = {Desmoplakin Maintains Transcellular Keratin Scaffolding
                    and Protects From Intestinal Injury},
  JournalTitle    = {Cell. Mol. Gastroenterol. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jcmgh.2021.12.009},
  Number          = {4},
  Pages           = {1181--1200},
  Volume          = {13}
}

@Article{Thamm2022-fu,
  Author          = {Thamm, Mirko and Rosenhain, Stefanie and Leonardic,
                    Kevin and Höfter, Andreas and Kiessling, Fabian and Osl,
                    Franz and Pöschinger, Thomas and Gremse, Felix},
  Title           = {Intrinsic Respiratory Gating for Simultaneous
                    Multi-Mouse {μCT} Imaging to Assess Liver Tumors},
  JournalTitle    = {Frontiers in Medicine},
  Date            = {2022},
  DOI             = {10.3389/fmed.2022.878966},
  Pages           = {878966},
  Volume          = {9}
}

@Article{Lemoinne2020-nb,
  Author          = {Lemoinne, Sara and Kemgang, Astrid and Ben Belkacem,
                    Karima and Straube, Marjolène and Jegou, Sarah and
                    Corpechot, Christophe and {Saint-Antoine IBD Network} and
                    Chazouillères, Olivier and Housset, Chantal and Sokol,
                    Harry},
  Title           = {Fungi participate in the dysbiosis of gut microbiota in
                    patients with primary sclerosing cholangitis},
  JournalTitle    = {Gut},
  Date            = {2019},
  DOI             = {10.1136/gutjnl-2018-317791},
  Number          = {1},
  Pages           = {92--102},
  Volume          = {69}
}

@Article{Richter2022-vy,
  Author          = {Richter, Beate and Zafarnia, Sarah and Gremse, Felix and
                    Kießling, Fabian and Scheuerlein, Hubert and Settmacher,
                    Utz and Dahmen, Uta},
  Title           = {Corrosion Cast and {3D} Reconstruction of the {Murine}
                    Biliary Tree After Biliary Obstruction: {Quantitative}
                    Assessment and Comparison With {2D} Histology},
  JournalTitle    = {J. Clin. Exp. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/j.jceh.2021.12.008},
  Number          = {3},
  Pages           = {755--766},
  Volume          = {12}
}

@Article{Martin-Mateos2021-xc,
  Author          = {Martín-Mateos, Rosa and Albillos, Agustín},
  Title           = {The Role of the Gut-Liver Axis in Metabolic
                    Dysfunction-Associated Fatty Liver Disease},
  JournalTitle    = {Front. Immunol.},
  Date            = {2021},
  DOI             = {10.3389/fimmu.2021.660179},
  Pages           = {660179},
  Volume          = {12}
}

@Article{Martin-Gallausiaux2021-xt,
  Author          = {Martin-Gallausiaux, Camille and Marinelli, Ludovica and
                    Blottière, Hervé M. and Larraufie, Pierre and Lapaque,
                    Nicolas},
  Title           = {{SCFA:} {Mechanisms} and functional importance in the
                    gut},
  JournalTitle    = {Proc. Nutr. Soc.},
  Date            = {2020},
  DOI             = {10.1017/s0029665120006916},
  Number          = {1},
  Pages           = {37--49},
  Volume          = {80}
}

@Article{Federici2022-fj,
  Author          = {Federici, Sara and Kredo-Russo, Sharon and Valdés-Mas,
                    Rafael and Kviatcovsky, Denise and Weinstock, Eyal and
                    Matiuhin, Yulia and Silberberg, Yael and Atarashi, Koji
                    and Furuichi, Munehiro and Oka, Akihiko and Liu, Bo and
                    Fibelman, Morine and Weiner, Iddo Nadav and Khabra, Efrat
                    and Cullin, Nyssa and Ben-Yishai, Noa and Inbar, Dana and
                    Ben-David, Hava and Nicenboim, Julian and Kowalsman, Noga
                    and Lieb, Wolfgang and Kario, Edith and Cohen, Tal and
                    Geffen, Yael Friedman and Zelcbuch, Lior and Cohen, Ariel
                    and Rappo, Urania and Gahali-Sass, Inbar and Golembo,
                    Myriam and Lev, Vered and Dori-Bachash, Mally and
                    Shapiro, Hagit and Moresi, Claudia and Cuevas-Sierra,
                    Amanda and Mohapatra, Gayatree and Kern, Lara and Zheng,
                    Danping and Nobs, Samuel Philip and Suez, Jotham and
                    Stettner, Noa and Harmelin, Alon and Zak, Naomi and
                    Puttagunta, Sailaja and Bassan, Merav and Honda, Kenya
                    and Sokol, Harry and Bang, Corinna and Franke, Andre and
                    Schramm, Christoph and Maharshak, Nitsan and Sartor, Ryan
                    Balfour and Sorek, Rotem and Elinav, Eran},
  Title           = {Targeted suppression of human {IBD}-associated gut
                    microbiota commensals by phage consortia for treatment of
                    intestinal inflammation},
  JournalTitle    = {Cell},
  Date            = {2022},
  DOI             = {10.1016/j.cell.2022.07.003},
  Number          = {16},
  Pages           = {2879--2898.e24},
  Volume          = {185}
}

@Article{Chu2020-hc,
  Author          = {Chu, Huikuan and Duan, Yi and Lang, Sonja and Jiang, Lu
                    and Wang, Yanhan and Llorente, Cristina and Liu, Jinyuan
                    and Mogavero, Selene and Bosques-Padilla, Francisco and
                    Abraldes, Juan G. and Vargas, Victor and Tu, Xin M. and
                    Yang, Ling and Hou, Xiaohua and Hube, Bernhard and
                    Stärkel, Peter and Schnabl, Bernd},
  Title           = {The Candida albicans exotoxin candidalysin promotes
                    alcohol-associated liver disease},
  JournalTitle    = {J. Hepatol.},
  Date            = {2020},
  DOI             = {10.1016/j.jhep.2019.09.029},
  Number          = {3},
  Pages           = {391--400},
  Volume          = {72}
}

@Article{Zuo:834142,
  Author          = {Zuo, Simin and Al Rawashdeh, Wa’el and Rosenhain,
                    Stefanie and Magnuska, Zuzanna and Gyamfuah, Yamoah Grace
                    and Kießling, Fabian and Gremse, Felix},
  Title           = {Mixing Matrix-corrected Whole-body Pharmacokinetic
                    Modeling Using Longitudinal Micro-computed Tomography and
                    Fluorescence-mediated Tomography},
  JournalTitle    = {Mol. Imaging Biol.},
  Date            = {2021},
  DOI             = {10.1007/s11307-021-01623-y},
  Keywords        = {,CRC1382-Project Q01,CRC1382-Project Q01,CRC1382-Project
                    Q01},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {6},
  Pages           = {963--974},
  Volume          = {23}
}

@Article{Zweers2011,
  Author          = {Zweers, Serge J.L.B. and Booij, Klaske A.C. and Komuta,
                    Mina and Roskams, Tania and Gouma, Dirk J. and Jansen,
                    Peter L.M. and Schaap, Frank G.},
  Title           = {The human gallbladder secretes fibroblast growth factor
                    19 into bile: {Towards} defining the role of fibroblast
                    growth factor 19 in the enterobiliary tract},
  JournalTitle    = {Hepatology},
  Date            = {2011},
  DOI             = {10.1002/hep.24702},
  Keywords        = {Schaap-Selection},
  Number          = {2},
  Pages           = {575--583},
  Volume          = {55}
}

@Article{Zweers2016,
  Author          = {Zweers, Serge J. and Shiryaev, Alexey and Komuta, Mina
                    and Vesterhus, Mette and Hov, Johannes R. and Perugorria,
                    María J. and de Waart, D. Rudi and Chang, Jung-Chin and
                    Tol, Shanna and te Velde, Anje A. and de Jonge, Wouter J.
                    and Banales, Jesus M. and Roskams, Tania and Beuers,
                    Ulrich and Karlsen, Tom H. and Jansen, Peter L. and
                    Schaap, Frank G.},
  Title           = {Elevated interleukin-8 in bile of patients with primary
                    sclerosing cholangitis},
  JournalTitle    = {Liver Int.},
  Date            = {2016},
  DOI             = {10.1111/liv.13092},
  Number          = {9},
  Pages           = {1370--1377},
  Volume          = {36}
}

@Article{Zysow1997,
  Author          = {Zysow, Bernice R. and Kauser, Katalin and Lawn, Richard
                    M. and Rubanyi, Gabor M.},
  Title           = {Effects of Estrus Cycle, Ovariectomy, and Treatment with
                    Estrogen, Tamoxifen, and Progesterone on
                    Apolipoprotein(a) Gene Expression in Transgenic Mice},
  JournalTitle    = { Arterioscl. Throm. Vas.},
  Date            = {1997},
  DOI             = {10.1161/01.atv.17.9.1741},
  Keywords        = {Animals; Apolipoproteins/blood/*genetics; Apoprotein(a);
                    Drug Combinations; Estradiol Congeners/*pharmacology;
                    Estrogen Antagonists/*pharmacology; Estrus/*physiology;
                    Ethinyl Estradiol/*pharmacology; Female; Gene
                    Expression/*drug effects/physiology; *Lipoprotein(a);
                    Liver/metabolism; Mice; Mice,Transgenic/genetics;
                    Ovariectomy; Progesterone/*pharmacology;
                    RNA,Messenger/metabolism; Tamoxifen/*pharmacology},
  Note            = {Zysow, B R Kauser, K Lawn, R M Rubanyi, G M eng Research
                    Support, Non-U.S. Gov't Research Support, U.S. Gov't,
                    P.H.S. Arterioscler Thromb Vasc Biol. 1997
                    Sep;17(9):1741-5. doi: 10.1161/01.atv.17.9.1741.},
  Number          = {9},
  Pages           = {1741--1745},
  Volume          = {17}
}

@Article{adachi1995a,
  Author          = {Adachi, Yukito and Moore, Laura E. and Bradford, Blair
                    U. and Gao, Wenshi and Thurman, Ronald G.},
  Title           = {Antibiotics prevent liver injury in rats following
                    long-term exposure to ethanol},
  JournalTitle    = {Gastroenterology},
  Date            = {1995},
  DOI             = {10.1016/0016-5085(95)90027-6},
  Number          = {1},
  Pages           = {218--224},
  Volume          = {108}
}

@Article{ait2021a,
  Author          = {Ait Ahmed, Yeni and Fu, Yaojie and Rodrigues, Robim M.
                    and He, Yong and Guan, Yukun and Guillot, Adrien and Ren,
                    Ruixue and Feng, Dechun and Hidalgo, Juan and Ju, Cynthia
                    and Lafdil, Fouad and Gao, Bin},
  Title           = {Kupffer cell restoration after partial hepatectomy is
                    mainly driven by local cell proliferation in
                    {IL}-6-dependent autocrine and paracrine manners},
  JournalTitle    = {Cellular \& Molecular Immunology},
  Date            = {2021},
  DOI             = {10.1038/s41423-021-00731-7},
  Keywords        = {Guillot-Selection},
  Number          = {9},
  Pages           = {2165--2176},
  Volume          = {18}
}

@Article{al2017a,
  Author          = {Rawashdeh, Wa'el Al and Zuo, Simin and Melle, Andrea and
                    Appold, Lia and Koletnik, Susanne and Tsvetkova, Yoanna
                    and Beztsinna, Nataliia and Pich, Andrij and Lammers,
                    Twan and Kiessling, Fabian and Gremse, Felix},
  Title           = {Noninvasive Assessment of Elimination and Retention
                    using {CT}-{FMT} and Kinetic Whole-body Modeling},
  JournalTitle    = {Theranostics},
  Date            = {2017},
  DOI             = {10.7150/thno.17263},
  Number          = {6},
  Pages           = {1499--1510},
  Volume          = {7}
}

@Article{baier2019a,
  Author          = {Baier, Vanessa and Cordes, Henrik and Thiel, Christoph
                    and Castell, José V. and Neumann, Ulf P. and Blank, Lars
                    M. and Kuepfer, Lars},
  Title           = {A Physiology-Based Model of Human Bile Acid Metabolism
                    for Predicting Bile Acid Tissue Levels After Drug
                    Administration in Healthy Subjects and {BRIC} Type 2
                    Patients},
  JournalTitle    = {Front. Physiol.},
  Date            = {2019},
  DOI             = {10.3389/fphys.2019.01192},
  ids             = {Baier2019-oq},
  Keywords        = {Küpfer-Selection,Blank-Selection},
  Number          = {1192},
  Volume          = {10}
}

@Article{bajaj2017a,
  Author          = {Bajaj, Jasmohan S. and Kassam, Zain and Fagan, Andrew
                    and Gavis, Edith A. and Liu, Eric and Cox, I. Jane and
                    Kheradman, Raffi and Heuman, Douglas and Wang, Jessica
                    and Gurry, Thomas and Williams, Roger and Sikaroodi,
                    Masoumeh and Fuchs, Michael and Alm, Eric and John, Binu
                    and Thacker, Leroy R. and Riva, Antonio and Smith, Mark
                    and Taylor-Robinson, Simon D. and Gillevet, Patrick M},
  Title           = {Fecal microbiota transplant from a rational stool donor
                    improves hepatic encephalopathy: {A} randomized clinical
                    trial},
  JournalTitle    = {Hepatology},
  Date            = {2017},
  DOI             = {10.1002/hep.29306},
  Number          = {6},
  Pages           = {1727--1738},
  Subtitle        = {Bajaj et al.},
  Volume          = {66}
}

@Article{balmer2014a,
  Author          = {Balmer, Maria L. and Slack, Emma and de Gottardi, Andrea
                    and Lawson, Melissa A. E. and Hapfelmeier, Siegfried and
                    Miele, Luca and Grieco, Antonio and Van Vlierberghe, Hans
                    and Fahrner, René and Patuto, Nicola and Bernsmeier,
                    Christine and Ronchi, Francesca and Wyss, Madeleine and
                    Stroka, Deborah and Dickgreber, Nina and Heim, Markus H.
                    and McCoy, Kathy D. and Macpherson, Andrew J.},
  Title           = {The Liver May Act as a Firewall Mediating Mutualism
                    Between the Host and Its Gut Commensal Microbiota},
  JournalTitle    = {Sci. Transl. Med.},
  Date            = {2014},
  DOI             = {10.1126/scitranslmed.3008618},
  Number          = {237},
  Volume          = {6}
}

@Article{barker2007a,
  Author          = {Barker, Nick and van Es, Johan H. and Kuipers, Jeroen
                    and Kujala, Pekka and van den Born, Maaike and Cozijnsen,
                    Miranda and Haegebarth, Andrea and Korving, Jeroen and
                    Begthel, Harry and Peters, Peter J. and Clevers, Hans},
  Title           = {Identification of stem cells in small intestine and
                    colon by marker gene Lgr5},
  JournalTitle    = {Nature},
  Date            = {2007},
  DOI             = {10.1038/nature06196},
  Number          = {7165},
  Pages           = {1003--1007},
  Volume          = {449}
}

@Article{barnes2013a,
  Author          = {Barnes, M J and Griseri, T and Johnson, A M F and Young,
                    W and Powrie, F and Izcue, A},
  Title           = {{CTLA}-4 promotes Foxp3 induction and regulatory T cell
                    accumulation in the intestinal lamina propria},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2012},
  DOI             = {10.1038/mi.2012.75},
  Keywords        = {Izcue-Selection},
  Number          = {2},
  Pages           = {324--334},
  Volume          = {6}
}

@Article{barzakova2019a,
  Author          = {Barzakova, Emona S. and Schulze-Hagen, Maximilian and
                    Zimmermann, Markus and Lurje, Georg and Bednarsch, Jan
                    and Pedersoli, Federico and Isfort, Peter and Kuhl,
                    Christiane and Bruners, Philipp},
  Title           = {Monitoring Liver Function of Patients Undergoing
                    Transarterial Chemoembolization {(TACE)} by a {13C}
                    Breath Test {(LiMAx)}},
  JournalTitle    = {CardioVasc. Interv. Radiol.},
  Date            = {2019},
  DOI             = {10.1007/s00270-019-02325-3},
  Addendum        = preliminarywork,
  Keywords        = {Barzakova-Selection},
  Number          = {12},
  Pages           = {1702--1708},
  Volume          = {42}
}

@Article{barzakova2021a,
  Author          = {Barzakova, Emona and Senthilvel, Niveditha and Bruners,
                    Philipp and Keil, Sebastian and Lurje, Georg and
                    Zimmermann, Markus and Kuhl, Christiane K and Isfort,
                    Peter},
  Title           = {Detectability of Target Lesion During {CT}-Guided Tumor
                    Ablations: {Impact} on Ablation Outcome},
  JournalTitle    = {RöFo - Fortschritte auf dem Gebiet der Röntgenstrahlen
                    und der bildgebenden Verfahren},
  Date            = {2021},
  DOI             = {10.1055/a-1669-9342},
  Addendum        = preliminarywork,
  Keywords        = {Barzakova-Selection},
  Number          = {05},
  Pages           = {515--520},
  Volume          = {194}
}

@Article{bauer2002a,
  Author          = {Bauer, Tilman M. and Schwacha, Henning and
                    Steinbruckner, Bernhard and Brinkmann, Folke E. and
                    Ditzen, Anette K. and Aponte, John J. and Pelz, Klaus and
                    Berger, Dieter and Kist, Manfred and Blum, Hubert E.},
  Title           = {Small intestinal bacterial overgrowth in human cirrhosis
                    is associated with systemic endotoxemia},
  JournalTitle    = {Am. J. Gastroenterol.},
  Date            = {2002},
  DOI             = {10.1111/j.1572-0241.2002.05791.x},
  Number          = {9},
  Pages           = {2364--2370},
  Volume          = {97}
}

@Article{Smit1993-tl,
  Author          = {Smit, J.J.M. and Schinkel, A.H. and Elferink, R.P.J.Oude
                    and Groen, A.K. and Wagenaar, E. and van Deemter, L. and
                    Mol, C.A.A.M. and Ottenhoff, R. and van der Lugt, N.M.T.
                    and van Roon, M.A. and van der Valk, M.A. and Offerhaus,
                    G.J.A. and Berns, A.J.M. and Borst, P.},
  Title           = {Homozygous disruption of the murine {MDR2}
                    P-glycoprotein gene leads to a complete absence of
                    phospholipid from bile and to liver disease},
  JournalTitle    = {Cell},
  Date            = {1993},
  DOI             = {10.1016/0092-8674(93)90380-9},
  Number          = {3},
  Pages           = {451--462},
  Volume          = {75}
}

@Article{benede-ubieto2021a,
  Author          = {Benedé-Ubieto, Raquel and Estévez-Vázquez, Olga and
                    Guo, Feifei and Chen, Chaobo and Singh, Youvika and
                    Nakaya, Helder I. and Gómez del Moral, Manuel and
                    Lamas-Paz, Arantza and Morán, Laura and
                    López-Alcántara, Nuria and Reissing, Johanna and Bruns,
                    Tony and Avila, Matías A. and Santamaría, Eva and
                    Mazariegos, Marina S. and Woitok, Marius Maximilian and
                    Haas, Ute and Zheng, Kang and Juárez, Ignacio and
                    Martín-Villa, José Manuel and Asensio, Iris and
                    Vaquero, Javier and Peligros, Maria Isabel and Argemi,
                    Josepmaria and Bataller, Ramón and Ampuero, Javier and
                    Romero Gómez, Manuel and Trautwein, Christian and
                    Liedtke, Christian and Bañares, Rafael and Cubero,
                    Francisco Javier and Nevzorova, Yulia A.},
  Title           = {An Experimental \textsc{DUAL} Model of Advanced Liver
                    Damage},
  JournalTitle    = {Hepatology Communications},
  Date            = {2021},
  DOI             = {10.1002/hep4.1698},
  Number          = {6},
  Pages           = {1051--1068},
  Volume          = {5}
}

@Article{berkell2021a,
  Author          = {Berkell, M. and Mysara, M. and Xavier, B.B. and
                    Werkhoven, C.H. and Monsieurs, P. and Lammens, C. and
                    Ducher, A. and Vehreschild, M.J.G.T. and Goossens, H. and
                    Gunzburg, J. and Bonten, M.J.M. and Malhotra-Kumar, S.},
  Title           = {Microbiota-based markers predictive of development of
                    Clostridioides difficile infection},
  JournalTitle    = {Nat. Commun.},
  Date            = {2021},
  DOI             = {10.1038/s41467-021-22302-0},
  Keywords        = {Vehreschild-Selection},
  Number          = {1},
  Volume          = {12}
}

@Article{bestfater2021a,
  Author          = {Bestfater, Christian and Vehreschild, Maria J.G.T. and
                    Stallmach, Andreas and Tüffers, Kester and Erhardt,
                    Andreas and Frank, Thorsten and Glück, Thomas and
                    Goeser, Felix and Sellge, Gernot and Solbach, Philipp and
                    Eisenlohr, Herbert and Storr, Martin},
  Title           = {Clinical effectiveness of bidirectional fecal microbiota
                    transfer in the treatment of recurrent Clostridioides
                    difficile infections},
  JournalTitle    = {Dig. Dis. Sci.},
  Date            = {2021},
  DOI             = {10.1016/j.dld.2021.02.022},
  Keywords        = {Vehreschild-Selection},
  Number          = {6},
  Pages           = {706--711},
  Volume          = {53}
}

@Article{bhat2016a,
  Author          = {Bhat, Mamatha and Arendt, Bianca M and Bhat, Venkat and
                    Renner, Eberhard L and Humar, Atul and Allard, Johane P},
  Title           = {Implication of the intestinal microbiome in
                    complications of cirrhosis},
  JournalTitle    = {World J. Hepatol.},
  Date            = {2016},
  DOI             = {10.4254/wjh.v8.i27.1128},
  Number          = {27},
  Pages           = {1128},
  Volume          = {8}
}

@Article{biehl2022a,
  Author          = {Biehl, Lena M. and Higgins, Paul G. and Stemler, Jannik
                    and Gilles, Meyke and Peter, Silke and Dörfel, Daniela
                    and Vogel, Wichard and Kern, Winfried V. and Gölz, Hanna
                    and Bertz, Hartmut and Rohde, Holger and Klupp, Eva-Maria
                    and Schafhausen, Philippe and Salmanton-García, Jon and
                    Stecher, Melanie and Wille, Julia and Liss, Blasius and
                    Xanthopoulou, Kyriaki and Zweigner, Janine and Seifert,
                    Harald and Vehreschild, Maria J.G.T.},
  Title           = {Impact of single-room contact precautions on acquisition
                    and transmission of vancomycin-resistant enterococci on
                    haematological and oncological wards, multicentre
                    cohort-study, Germany, {January−December} 2016},
  JournalTitle    = {Eurosurveillance},
  Date            = {2022},
  DOI             = {10.2807/1560-7917.es.2022.27.2.2001876},
  Issue           = {2},
  Keywords        = {Vehreschild-Selection},
  Number          = {2},
  Volume          = {27}
}

@Article{boursier2016a,
  Author          = {Boursier, Jérôme and Mueller, Olaf and Barret,
                    Matthieu and Machado, Mariana and Fizanne, Lionel and
                    Araujo-Perez, Felix and Guy, Cynthia D. and Seed, Patrick
                    C. and Rawls, John F. and David, Lawrence A. and Hunault,
                    Gilles and Oberti, Frédéric and Calès, Paul and Diehl,
                    Anna Mae},
  Title           = {The severity of nonalcoholic fatty liver disease is
                    associated with gut dysbiosis and shift in the metabolic
                    function of the gut microbiota},
  JournalTitle    = {Hepatology},
  Date            = {2016},
  DOI             = {10.1002/hep.28356},
  Number          = {3},
  Pages           = {764--775},
  Subtitle        = {Boursier et al.},
  Volume          = {63}
}

@Article{brol_combination_2019,
  Author          = {Brol, Maximilian Joseph and Rösch, Felicitas and
                    Schierwagen, Robert and Magdaleno, Fernando and Uschner,
                    Frank Erhard and Manekeller, Steffen and Queck, Alexander
                    and Schwarzkopf, Katharina and Odenthal, Margarete and
                    Drebber, Uta and Thiele, Maja and Lingohr, Philipp and
                    Plamper, Andreas and Kristiansen, Glen and Lotersztajn,
                    Sophie and Krag, Aleksander and Klein, Sabine and
                    Rheinwalt, Karl P. and Trebicka, Jonel},
  Title           = {Combination of CCl\textsubscript{4} with alcoholic and
                    metabolic injuries mimics human liver fibrosis},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2019},
  DOI             = {10.1152/ajpgi.00361.2018},
  Keywords        = {ASH,liver fibrosis,NAFLD,NASH},
  Number          = {2},
  Pages           = {G182--G194},
  URLDate         = {2022-08-25},
  Volume          = {317}
}

@Article{Brozat2022-em,
  Author          = {Brozat, Jonathan F and Hanses, Frank and Haelberger,
                    Martina and Stecher, Melanie and Dreher, Michael and
                    Tometten, Lukas and Ruethrich, Maria M and Vehreschild,
                    Janne J and Trautwein, Christian and Borgmann, Stefan and
                    Vehreschild, Maria J G T and Jakob, Carolin E M and
                    Stallmach, Andreas and Wille, Kai and Hellwig, Kerstin
                    and Isberner, Nora and Reuken, Philipp A and Geisler,
                    Fabian and Nattermann, Jacob and Bruns, Tony and {LEOSS
                    study group}},
  Title           = {{COVID-19} mortality in cirrhosis is determined by
                    cirrhosis-associated comorbidities and extrahepatic organ
                    failure: {Results} from the multinational {LEOSS}
                    registry},
  JournalTitle    = {United European Gastroenterol. J.},
  Date            = {2022},
  DOI             = {10.1002/ueg2.12232},
  Number          = {4},
  Pages           = {409--424},
  Volume          = {10}
}

@Article{brozat2022a,
  Author          = {Brozat, Jonathan Frederik and Brandt, Elisa and Stark,
                    Myriam and Fischer, Petra and Wirtz, Theresa Hildegard
                    and Flaßhove, Alexander and Rodenhausen, Aaron Nikolai
                    and Vajen, Tanja and Heinzmann, Alexandra C.A. and
                    Schmitz, Sophia M. and Jhaisha, Samira Abu and Röth,
                    Anjali A. and Koenen, Rory R. and Sahin, Hacer and
                    Trautwein, Christian and Berres, Marie-Luise},
  Title           = {{JAM}-A is a multifaceted regulator in hepatic
                    fibrogenesis, supporting {LSEC} integrity and stellate
                    cell quiescence},
  JournalTitle    = {J. Hepatol.},
  Date            = {2022},
  DOI             = {10.1016/s0168-8278(22)00760-7},
  ids             = {Brozat2022-zs},
  Keywords        = {Wirtz-Selection,Berres-Selection},
  Pages           = {S193},
  Volume          = {77}
}

@Article{brugiroux2016a,
  Author          = {Brugiroux, Sandrine and Beutler, Markus and Pfann,
                    Carina and Garzetti, Debora and Ruscheweyh, Hans-Joachim
                    and Ring, Diana and Diehl, Manuel and Herp, Simone and
                    Lötscher, Yvonne and Hussain, Saib and Bunk, Boyke and
                    Pukall, Rüdiger and Huson, Daniel H. and Münch, Philipp
                    C. and McHardy, Alice C. and McCoy, Kathy D. and
                    Macpherson, Andrew J. and Loy, Alexander and Clavel,
                    Thomas and Berry, David and Stecher, Bärbel},
  Title           = {Genome-guided design of a defined mouse microbiota that
                    confers colonization resistance against Salmonella
                    enterica serovar Typhimurium},
  JournalTitle    = {Nat. Microbiol.},
  Date            = {2016},
  DOI             = {10.1038/nmicrobiol.2016.215},
  Number          = {2},
  Volume          = {2}
}

@Article{bucheli2021a,
  Author          = {Bucheli, Olivia T. M. and Sigvaldadóttir, Ingibjörg
                    and Eyer, Klaus},
  Title           = {Measuring single‐cell protein secretion in immunology:
                    {Technologies,} advances, and applications},
  JournalTitle    = {Eur. J. Immunol.},
  Date            = {2021},
  DOI             = {10.1002/eji.202048976},
  Number          = {6},
  Pages           = {1334--1347},
  Volume          = {51}
}

@Article{bunker2015a,
  Author          = {Bunker, Jeffrey J. and Flynn, Theodore M. and Koval,
                    Jason C. and Shaw, Dustin G. and Meisel, Marlies and
                    McDonald, Benjamin D. and Ishizuka, Isabel E. and Dent,
                    Alexander L. and Wilson, Patrick C. and Jabri, Bana and
                    Antonopoulos, Dionysios A. and Bendelac, Albert},
  Title           = {Innate and Adaptive Humoral Responses Coat Distinct
                    Commensal Bacteria with Immunoglobulin A},
  JournalTitle    = {Immunity},
  Date            = {2015},
  DOI             = {10.1016/j.immuni.2015.08.007},
  Number          = {3},
  Pages           = {541--553},
  Volume          = {43}
}

@Article{bunker2017a,
  Author          = {Bunker, Jeffrey J. and Erickson, Steven A. and Flynn,
                    Theodore M. and Henry, Carole and Koval, Jason C. and
                    Meisel, Marlies and Jabri, Bana and Antonopoulos,
                    Dionysios A. and Wilson, Patrick C. and Bendelac,
                    Albert},
  Title           = {Natural polyreactive {IgA} antibodies coat the
                    intestinal microbiota},
  JournalTitle    = {Science},
  Date            = {2017},
  DOI             = {10.1126/science.aan6619},
  Number          = {6361},
  Volume          = {358}
}

@Article{candels2021a,
  Author          = {Candels, Lena S. and Rahim, Mussarat N. and Shah, Sital
                    and Heneghan, Michael A.},
  Title           = {Towards personalised medicine in autoimmune hepatitis:
                    {Measurement} of thiopurine metabolites results in higher
                    biochemical response rates},
  JournalTitle    = {J. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jhep.2021.03.023},
  Keywords        = {Candels-Selection},
  Number          = {2},
  Pages           = {324--332},
  Volume          = {75}
}

@Article{candels2022a,
  Author          = {Candels, Lena Susanna and Becker, Svea and Trautwein,
                    Christian},
  Title           = {{PLA2G7:} {A} new player in shaping energy metabolism
                    and lifespan},
  JournalTitle    = {Signal Transduct. Target. Ther.},
  Date            = {2022},
  DOI             = {10.1038/s41392-022-01052-5},
  Keywords        = {Candels-Selection,Trautwein-Selection},
  Number          = {1},
  Volume          = {7}
}

@Article{cario2013a,
  Author          = {Cario, Elke},
  Title           = {Microbiota and innate immunity in intestinal
                    inflammation and neoplasia},
  JournalTitle    = {Curr. Opin. Gastroenterol.},
  Date            = {2013},
  DOI             = {10.1097/mog.0b013e32835a670e},
  Number          = {1},
  Pages           = {85--91},
  Volume          = {29}
}

@Article{cerovic2015a,
  Author          = {Cerovic, V and Houston, S A and Westlund, J and
                    Utriainen, L and Davison, E S and Scott, C L and Bain, C
                    C and Joeris, T and Agace, W W and Kroczek, R A and
                    Mowat, A M and Yrlid, U and Milling, S WF},
  Title           = {Lymph-borne {CD8α+} dendritic cells are uniquely able
                    to cross-prime {CD8+} T cells with antigen acquired from
                    intestinal epithelial cells},
  JournalTitle    = {Mucosal Immunol.},
  Date            = {2014},
  DOI             = {10.1038/mi.2014.40},
  Number          = {1},
  Pages           = {38--48},
  Volume          = {8}
}

@Article{chen2011a,
  Author          = {Chen, Yanfei and Yang, Fengling and Lu, Haifeng and
                    Wang, Baohong and Chen, Yunbo and Lei, Dajiang and Wang,
                    Yuezhu and Zhu, Baoli and Li, Lanjuan},
  Title           = {Characterization of fecal microbial communities in
                    patients with liver cirrhosis},
  JournalTitle    = {Hepatology},
  Date            = {2011},
  DOI             = {10.1002/hep.24423},
  Number          = {2},
  Pages           = {562--572},
  Volume          = {54}
}

@Article{claus2008a,
  Author          = {Claus, Sandrine P and Tsang, Tsz M and Wang, Yulan and
                    Cloarec, Olivier and Skordi, Eleni and Martin,
                    François‐Pierre and Rezzi, Serge and Ross, Alastair
                    and Kochhar, Sunil and Holmes, Elaine and Nicholson,
                    Jeremy K},
  Title           = {Systemic multicompartmental effects of the gut
                    microbiome on mouse metabolic phenotypes},
  JournalTitle    = {Mol. Syst. Biol.},
  Date            = {2008},
  DOI             = {10.1038/msb.2008.56},
  Number          = {1},
  Pages           = {219},
  Volume          = {4}
}

@Article{dapito2012a,
  Author          = {Dapito, Dianne H. and Mencin, Ali and Gwak, Geum-Youn
                    and Pradere, Jean-Philippe and Jang, Myoung-Kuk and
                    Mederacke, Ingmar and Caviglia, Jorge M. and Khiabanian,
                    Hossein and Adeyemi, Adebowale and Bataller, Ramon and
                    Lefkowitch, Jay H. and Bower, Maureen and Friedman,
                    Richard and Sartor, R. Balfour and Rabadan, Raul and
                    Schwabe, Robert F.},
  Title           = {Promotion of Hepatocellular Carcinoma by the Intestinal
                    Microbiota and {TLR4}},
  JournalTitle    = {Cancer Cell},
  Date            = {2012},
  DOI             = {10.1016/j.ccr.2012.02.007},
  Number          = {4},
  Pages           = {504--516},
  Volume          = {21}
}

@Article{dawson2017a,
  Author          = {Dawson, Paul A.},
  Title           = {Hepatic bile acid uptake in humans and mice: {Multiple}
                    pathways and expanding potential role for gut‐liver
                    signaling},
  JournalTitle    = {Hepatology},
  Date            = {2017},
  DOI             = {10.1002/hep.29325},
  Number          = {5},
  Pages           = {1384--1386},
  Volume          = {66}
}

@Article{dogan2009a,
  Author          = {Dogan, Ismail and Bertocci, Barbara and Vilmont,
                    Valérie and Delbos, Frédéric and Mégret, Jérome and
                    Storck, Sébastien and Reynaud, Claude-Agnès and Weill,
                    Jean-Claude},
  Title           = {Multiple layers of B cell memory with different effector
                    functions},
  JournalTitle    = {Nat. Immunol.},
  Date            = {2009},
  DOI             = {10.1038/ni.1814},
  Number          = {12},
  Pages           = {1292--1299},
  Volume          = {10}
}

@Article{dudek2021a,
  Author          = {Dudek, M. and Pfister, D. and Donakonda, S. and Filpe,
                    P. and Schneider, A. and Laschinger, M. and Hartmann, D.
                    and Huser, N. and Meiser, P. and Bayerl, F. and Inverso,
                    D. and Wigger, J. and Sebode, M. and Ollinger, R. and
                    Rad, R. and Hegenbarth, S. and Anton, M. and Guillot, A.
                    and Bowman, A. and Heide, D. and Muller, F. and Ramadori,
                    P. and Leone, V. and Garcia-Caceres, C. and Gruber, T.
                    and Seifert, G. and Kabat, A.M. and Mallm, J.P. and
                    Reider, S. and Effenberger, M. and Roth, S. and Billeter,
                    A.T. and Muller-Stich, B. and Pearce, E.J. and
                    Koch-Nolte, F. and Kaser, R. and Tilg, H. and Thimme, R.
                    and Boettler, T. and Tacke, F. and Dufour, J.F. and
                    Haller, D. and Murray, P.J. and Heeren, R. and Zehn, D.
                    and Bottcher, J.P. and Heikenwalder, M. and Knolle,
                    P.A.},
  Title           = {Auto-aggressive {CXCR6(+)} {CD8} T cells cause liver
                    immune pathology in {NASH}},
  JournalTitle    = {Nature},
  Date            = {2021},
  DOI             = {10.1038/s41586-021-03233-8},
  Keywords        = {Guillot-Selection},
  Pages           = {444--449},
  Volume          = {592}
}

@Article{Dumas2006,
  Author          = {Dumas, Marc-Emmanuel and Barton, Richard H. and Toye,
                    Ayo and Cloarec, Olivier and Blancher, Christine and
                    Rothwell, Alice and Fearnside, Jane and Tatoud, Roger and
                    Blanc, Véronique and Lindon, John C. and Mitchell, Steve
                    C. and Holmes, Elaine and McCarthy, Mark I. and Scott,
                    James and Gauguier, Dominique and Nicholson, Jeremy K.},
  Title           = {Metabolic profiling reveals a contribution of gut
                    microbiota to fatty liver phenotype in insulin-resistant
                    mice},
  Date            = {2006-08},
  DOI             = {10.1073/pnas.0601056103},
  Number          = {33},
  Pages           = {12511--12516},
  Volume          = {103}
}

@Article{dupont2016a,
  Author          = {Dupont, Aline and Sommer, Felix and Zhang, Kaiyi and
                    Repnik, Urska and Basic, Marijana and Bleich, André and
                    Kühnel, Mark and Bäckhed, Fredrik and Litvak, Yael and
                    Fulde, Marcus and Rosenshine, Ilan and Hornef, Mathias
                    W.},
  Title           = {Age-Dependent Susceptibility to Enteropathogenic
                    {Escherichia} coli {(EPEC)} Infection in Mice},
  JournalTitle    = {PLoS Pathog.},
  Date            = {2016},
  DOI             = {10.1371/journal.ppat.1005616},
  Number          = {5},
  Pages           = {e1005616},
  Volume          = {12}
}

@Article{dyson2018a,
  Author          = {Dyson, Jessica K and Beuers, Ulrich and Jones, David E J
                    and Lohse, Ansgar W and Hudson, Mark},
  Title           = {Primary sclerosing cholangitis},
  JournalTitle    = {The Lancet},
  Date            = {2018},
  DOI             = {10.1016/s0140-6736(18)30300-3},
  Number          = {10139},
  Pages           = {2547--2559},
  Volume          = {391}
}

@Article{ehedego2018a,
  Author          = {Ehedego, Haksier and Mohs, Antje and Jansen, Bettina and
                    Hiththetiya, Kanishka and Sicinski, Piotr and Liedtke,
                    Christian and Trautwein, Christian},
  Title           = {Loss of Cyclin E1 attenuates hepatitis and
                    hepatocarcinogenesis in a mouse model of chronic liver
                    injury},
  JournalTitle    = {Oncogene},
  Date            = {2018},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1038/s41388-018-0181-8},
  Keywords        = {Mohs-Selection},
  Addendum        = equal,
  Number          = {25},
  Pages           = {3329--3339},
  Volume          = {37}
}

@Article{eksteen2004a,
  Author          = {Eksteen, Bertus and Grant, Allister J. and Miles, Alice
                    and Curbishley, Stuart M. and Lalor, Patricia F. and
                    Hübscher, Stefan G. and Briskin, Michael and Salmon,
                    Mike and Adams, David H.},
  Title           = {Hepatic Endothelial {CCL25} Mediates the Recruitment of
                    {CCR9+} Gut-homing Lymphocytes to the Liver in Primary
                    Sclerosing Cholangitis},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2004},
  DOI             = {10.1084/jem.20041035},
  Number          = {11},
  Pages           = {1511--1517},
  Volume          = {200}
}

@Article{elinav2018a,
  Author          = {Elinav, Eran and Henao-Mejia, Jorge and Strowig, Till
                    and Flavell, Richard},
  Title           = {{NLRP6} and Dysbiosis: {Avoiding} the Luring Attraction
                    of Over-Simplification},
  JournalTitle    = {Immunity},
  Date            = {2018},
  DOI             = {10.1016/j.immuni.2018.04.002},
  Number          = {4},
  Pages           = {603--604},
  Volume          = {48}
}

@Article{farowski2019a,
  Author          = {Farowski, Fedja and Solbach, Philipp and Tsakmaklis,
                    Anastasia and Brodesser, Susanne and Cruz Aguilar, M.
                    Rebeca and Cornely, Oliver A. and Dettmer, Katja and
                    Higgins, Paul G. and Suerbaum, Sebastian and Jazmati,
                    Nathalie and Oefner, Peter J. and Vehreschild, Maria
                    J.G.T.},
  Title           = {Potential biomarkers to predict outcome of faecal
                    microbiota transfer for recurrent Clostridioides
                    difficile infection},
  JournalTitle    = {Dig. Dis. Sci.},
  Date            = {2019},
  DOI             = {10.1016/j.dld.2019.01.012},
  Keywords        = {Vehreschild-Selection},
  Number          = {7},
  Pages           = {944--951},
  Volume          = {51}
}

@Article{fendt2021a,
  Author          = {Fendt, Rebekka and Hofmann, Ute and Schneider, Annika R.
                    P. and Schaeffeler, Elke and Burghaus, Rolf and Yilmaz,
                    Ali and Blank, Lars Mathias and Kerb, Reinhold and
                    Lippert, Jörg and Schlender, Jan-Frederik and Schwab,
                    Matthias and Kuepfer, Lars},
  Title           = {Data-driven personalization of a physiologically based
                    pharmacokinetic model for caffeine: {A} systematic
                    assessment},
  JournalTitle    = {CPT: Pharmacomet. Syst. Pharmacol.},
  Date            = {2021},
  DOI             = {10.1002/psp4.12646},
  Keywords        = {Küpfer-Selection},
  Number          = {7},
  Pages           = {782--793},
  Volume          = {10}
}

@Article{Niu2022-al,
  Author          = {Niu, Lili and Geyer, Philipp E and Gupta, Rajat and
                    Santos, Alberto and Meier, Florian and Doll, Sophia and
                    Wewer Albrechtsen, Nicolai J and Klein, Sabine and Ortiz,
                    Cristina and Uschner, Frank E and Schierwagen, Robert and
                    Trebicka, Jonel and Mann, Matthias},
  DOI             = {10.15252/msb.202210947},
  Year            = {2022},
  Volume          = {18},
  Number          = {5},
  Title           = {Dynamic human liver proteome atlas reveals functional
                    insights into disease pathways},
  JournalTitle    = {Mol. Syst. Biol.},
  Keywords = {Trebicka-Selection}
}


@Article{gao2019a,
  Author          = {Gao, Yanhang and Zhou, Zhou and Ren, Tianyi and Kim,
                    Seung-Jin and He, Yong and Seo, Wonhyo and Guillot,
                    Adrien and Ding, Yanhua and Wu, Ruihong and Shao, Shuang
                    and Wang, Xiaomei and Zhang, Hong and Wang, Wei and Feng,
                    Dechun and Xu, Mingjiang and Han, Elaine and Zhong, Wei
                    and Zhou, Zhanxiang and Pacher, Pal and Niu, Junqi and
                    Gao, Bin},
  Title           = {Alcohol inhibits T-cell glucose metabolism and hepatitis
                    in {ALDH2}-deficient mice and humans: {Roles} of
                    acetaldehyde and glucocorticoids},
  JournalTitle    = {Gut},
  Date            = {2018},
  DOI             = {10.1136/gutjnl-2018-316221},
  Keywords        = {Guillot-Selection},
  Number          = {7},
  Pages           = {1311--1322},
  Volume          = {68}
}

@Article{gasmi2022a,
  Author          = {Gasmi, Imène and Machou, Camilia and Rodrigues,
                    Aurélie and Brouillet, Arthur and Nguyen, Trung Cong and
                    Rousseau, Benoit and Guillot, Adrien and Rodriguez,
                    Christophe and Demontant, Vanessa and Ait-Ahmed, Yeni and
                    Calderaro, Julien and Luciani, Alain and Pawlotsky,
                    Jean-Michel and Lafdil, Fouad},
  Title           = {Interleukin-17 programs liver progenitor cell
                    transformation into cancer stem cells through mir-122
                    downregulation with increased risk of primary liver
                    cancer initiation},
  JournalTitle    = {Int. J. Biol. Sci.},
  Date            = {2022},
  DOI             = {10.7150/ijbs.70408},
  Keywords        = {Guillot-Selection},
  Number          = {5},
  Pages           = {1944--1960},
  Volume          = {18}
}

@Article{giannelli2014a,
  Author          = {Giannelli, Valerio},
  Title           = {Microbiota and the gut-liver axis: {Bacterial}
                    translocation, inflammation and infection in cirrhosis},
  JournalTitle    = {World J. Gastroenterol.},
  Date            = {2014},
  DOI             = {10.3748/wjg.v20.i45.16795},
  Number          = {45},
  Pages           = {16795},
  Volume          = {20}
}

@Article{grognot-in-preparation-a,
  Author          = {Grognot, Marianne and Nelson, L. and Taute, K. M.},
  Title           = {\emph{Vibrio alginolyticus} flagellar systems act
                    synergistically in navigating complex environments},
  PubState        = {inpreparation}
}

@Article{grognot-in-preparation-b,
  Author          = {Grognot, Marianne and Taute, K. M.},
  Title           = {Geometry amplifies phenotypic diversity in navigation
                    behaviours},
  PubState        = {inpreparation}
}

@Article{grognot2021a,
  Author          = {Grognot, Marianne and Taute, Katja M.},
  Title           = {A multiscale {3D} chemotaxis assay reveals bacterial
                    navigation mechanisms},
  JournalTitle    = {Commun. Biol.},
  Date            = {2021},
  DOI             = {10.1038/s42003-021-02190-2},
  Keywords        = {Grognot-Selection},
  Number          = {1},
  Pages           = {669},
  Volume          = {4}
}

@Article{grognot2021b,
  Author          = {Grognot, Marianne and Taute, Katja M},
  Title           = {More than propellers: {How} flagella shape bacterial
                    motility behaviors},
  JournalTitle    = {Curr. Opin. Microbiol.},
  Date            = {2021},
  DOI             = {10.1016/j.mib.2021.02.005},
  ids             = {Grognot2021More},
  Keywords        = {Grognot-Selection},
  Pages           = {73--81},
  Volume          = {61}
}

@Article{grognot2021c,
  Author          = {Grognot, Marianne and Mittal, Anisha and Mah’moud,
                    Mattia and Taute, Katja M.},
  Title           = {Vibrio cholerae Motility in Aquatic and Mucus-Mimicking
                    Environments},
  JournalTitle    = {Appl. Environ. Microbiol.},
  Date            = {2021},
  DOI             = {10.1128/aem.01293-21},
  Keywords        = {Grognot-Selection},
  Number          = {20},
  Pages           = {01293--21},
  Volume          = {87}
}

@Article{guillot2014a,
  Author          = {Guillot, Adrien and Hamdaoui, Nabila and Bizy, Alexandra
                    and Zoltani, Keve and Souktani, Rachid and Zafrani,
                    Elie-Serge and Mallat, Ariane and Lotersztajn, Sophie and
                    Lafdil, Fouad},
  Title           = {Cannabinoid receptor 2 counteracts
                    interleukin-17-induced immune and fibrogenic responses in
                    mouse liver},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26598},
  Keywords        = {Guillot-Selection},
  Number          = {1},
  Pages           = {296--306},
  Subtitle        = {Guillot et al.},
  Volume          = {59}
}

@Article{guillot2019a,
  Author          = {Guillot, Adrien and Ren, Tianyi and Jourdan, Tony and
                    Pawlosky, Robert J. and Han, Elaine and Kim, Seung-Jin
                    and Zhang, Li and Koob, George F. and Gao, Bin},
  Title           = {Targeting liver aldehyde dehydrogenase-2 prevents heavy
                    but not moderate alcohol drinking},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2019},
  DOI             = {10.1073/pnas.1908137116},
  Keywords        = {Guillot-Selection},
  Number          = {51},
  Pages           = {25974--25981},
  Volume          = {116}
}

@Article{guo2009a,
  Author          = {Guo, Jun and Longshore, Shannon and Nair, Rajalakshmi
                    and Warner, Brad W.},
  Title           = {Retinoblastoma Protein {(pRb),} but Not p107 or p130, Is
                    Required for Maintenance of Enterocyte Quiescence and
                    Differentiation in Small Intestine},
  JournalTitle    = {J. Biol. Chem.},
  Date            = {2009},
  DOI             = {10.1074/jbc.m806133200},
  Number          = {1},
  Pages           = {134--140},
  Volume          = {284}
}

@Article{guo2021a,
  Author          = {Guo, Yuchen and Gabola, Monica and Lattanzio, Rossano
                    and Paul, Conception and Pinet, Valérie and Tang, Ruizhi
                    and Turali, Hulya and Bremond, Julie and Longobardi, Ciro
                    and Maurizy, Chloé and Da Costa, Quentin and Finetti,
                    Pascal and Boissière-Michot, Florence and Rivière,
                    Benjamin and Lemmers, Céline and Garnier, Séverine and
                    Bertucci, François and Zlobec, Inti and Chebli, Karim
                    and Tazi, Jamal and Azar, Rania and Blanchard, Jean-Marie
                    and Sicinski, Peter and Mamessier, Emilie and Lemmers,
                    Bénédicte and Hahne, Michael},
  Title           = {Cyclin A2 maintains colon homeostasis and is a
                    prognostic factor in colorectal cancer},
  JournalTitle    = {J. Clin. Invest.},
  Date            = {2021},
  DOI             = {10.1172/jci131517},
  Number          = {4},
  Volume          = {131}
}

@Article{hammerschmidt2008a,
  Author          = {Hammerschmidt, Swantje I. and Ahrendt, Manuela and Bode,
                    Ulrike and Wahl, Benjamin and Kremmer, Elisabeth and
                    Förster, Reinhold and Pabst, Oliver},
  Title           = {Stromal mesenteric lymph node cells are essential for
                    the generation of gut-homing T cells in vivo},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2008},
  DOI             = {10.1084/jem.20080039},
  ids             = {Hammerschmidt:789320},
  Number          = {11},
  Pages           = {2483--2490},
  Volume          = {205}
}

@Article{he2019a,
  Author          = {He, Yong and Hwang, Seonghwan and Cai, Yan and Kim,
                    Seung‐Jin and Xu, Mingjiang and Yang, Dingcheng and
                    Guillot, Adrien and Feng, Dechun and Seo, Wonhyo and Hou,
                    Xin and Gao, Bin},
  Title           = {{MicroRNA‐223} Ameliorates Nonalcoholic
                    Steatohepatitis and Cancer by Targeting Multiple
                    Inflammatory and Oncogenic Genes in Hepatocytes},
  JournalTitle    = {Hepatology},
  Date            = {2019},
  DOI             = {10.1002/hep.30645},
  Keywords        = {Guillot-Selection},
  Number          = {4},
  Pages           = {1150--1167},
  Volume          = {70}
}

@Article{henao-mejia2012a,
  Author          = {Henao-Mejia, Jorge and Elinav, Eran and Jin, Chengcheng
                    and Hao, Liming and Mehal, Wajahat Z. and Strowig, Till
                    and Thaiss, Christoph A. and Kau, Andrew L. and
                    Eisenbarth, Stephanie C. and Jurczak, Michael J. and
                    Camporez, Joao-Paulo and Shulman, Gerald I. and Gordon,
                    Jeffrey I. and Hoffman, Hal M. and Flavell, Richard A.},
  Title           = {Inflammasome-mediated dysbiosis regulates progression of
                    {NAFLD} and obesity},
  JournalTitle    = {Nature},
  Date            = {2012},
  DOI             = {10.1038/nature10809},
  ids             = {Henao-Mejia2012Inflammasome-mediated},
  Number          = {7384},
  Pages           = {179--185},
  Volume          = {482}
}

@Article{izcue2008a,
  Author          = {Izcue, Ana and Hue, Sophie and Buonocore, Sofia and
                    Arancibia-Cárcamo, Carolina V. and Ahern, Philip P. and
                    Iwakura, Yoichiro and Maloy, Kevin J. and Powrie, Fiona},
  Title           = {Interleukin-23 Restrains Regulatory T Cell Activity to
                    Drive T Cell-Dependent Colitis},
  Addendum        = equal,
  JournalTitle    = {Immunity},
  Date            = {2008},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1016/j.immuni.2008.02.019},
  Keywords        = {Izcue-Selection},
  Number          = {4},
  Pages           = {559--570},
  Volume          = {28}
}

@Article{izcue2009a,
  Author          = {Izcue, Ana and Coombes, Janine L. and Powrie, Fiona},
  Title           = {Regulatory Lymphocytes and Intestinal Inflammation},
  JournalTitle    = {Annu. Rev. Immunol.},
  Date            = {2009},
  DOI             = {10.1146/annurev.immunol.021908.132657},
  Keywords        = {Izcue-Selection},
  Number          = {1},
  Pages           = {313--338},
  Volume          = {27}
}

@Patent{Clavel-patent,
  Title           = {Synthetic communities of cultured bacteria for chicken},
  Date            = {2021},
  Number          = {DE1020212009034}
}

@Patent{jankowski-patent1,
  Title           = {Process for the removal of protein-bound toxins from the
                    blood of uraemic patients},
  Number          = {102011078700.3}
}

@Patent{jankowski-patent2,
  Title           = {Process for the removal of protein-bound toxins from the
                    blood of chronic renal failure using high-frequency
                    electric fields},
  Number          = {DE 10 2012 025 164.5/US-Ser. No. 61/740026}
}

@Patent{jankowski-patent3,
  Title           = {Perfusion for the co-culture of endothelial cells and
                    smooth muscle cells to determine changes in the vascular
                    pathophysiology},
  Number          = {P678009DE}
}

@Patent{jankowski-patent4,
  Title           = {Diagnosis of chronic kidney disease by quantitative
                    analysis of post-translational modifications of plasma
                    proteins},
  Number          = {PCT/EP2015/057761}
}

@Patent{jankowski-patent5,
  Title           = {Cardioprotective effect of vasoconstriction-inhibiting
                    factor (VIF)},
  Date            = {2020},
  Number          = {WO 2020/161158}
}

@Article{LlaCid2021,
  Author          = {Llaó-Cid, Laura and Roessner, Philipp M. and
                    Chapaprieta, Vicente and Öztürk, Selcen and Roider,
                    Tobias and Bordas, Marie and Izcue, Ana and Colomer,
                    Dolors and Dietrich, Sascha and Stilgenbauer, Stephan and
                    Hanna, Bola and Martı́n-Subero, José Ignacio and
                    Seiffert, Martina},
  Title           = {{EOMES} is essential for antitumor activity of {CD}8+ T
                    cells in chronic lymphocytic leukemia},
  JournalTitle    = {Leukemia},
  Date            = {2021},
  Addendum        = preliminarywork,
  DOI             = {10.1038/s41375-021-01198-1},
  Number          = {11},
  Pages           = {3152--3162},
  Volume          = {35}
}

@Article{Kather2019,
  Author          = {Kather, Jakob Nikolas and Pearson, Alexander T. and
                    Halama, Niels and Jäger, Dirk and Krause, Jeremias and
                    Loosen, Sven H. and Marx, Alexander and Boor, Peter and
                    Tacke, Frank and Neumann, Ulf Peter and Grabsch, Heike I.
                    and Yoshikawa, Takaki and Brenner, Hermann and
                    Chang-Claude, Jenny and Hoffmeister, Michael and
                    Trautwein, Christian and Luedde, Tom},
  Title           = {Deep learning can predict microsatellite instability
                    directly from histology in gastrointestinal cancer},
  JournalTitle    = {Nat. Med.},
  Addendum        = preliminarywork,
  Date            = {2019},
  DOI             = {10.1038/s41591-019-0462-y},
  Number          = {7},
  Pages           = {1054--1056},
  Volume          = {25}
}

@Patent{jankowski-patent6,
  Title           = {Peptides for preventing or treating heart and blood
                    vessels disease},
  Date            = {2022},
  Number          = {WO 2022/136437; PCT/EP2021/087089}
}

@Article{Jiao2021,
  Author          = {Jiao, Long and Eickhoff, Roman and Egners, Antje and
                    Jumpertz, Sandra and Roth, Johanna and Erdem, Merve and
                    Kroh, Andreas and Duimel, Hans and López-Iglesias,
                    Carmen and Caro, Pilar and Heij, Lara R and Schmeding,
                    Maximilian and Meierhofer, David and Neumann, Ulf P and
                    Cramer, Thorsten},
  Title           = {Deletion of {mTOR} in liver epithelial cells enhances
                    hepatic metastasis of colon cancer},
  JournalTitle    = {J. Pathol.},
  Date            = {2021},
  Addendum        = preliminarywork,
  DOI             = {10.1002/path.5768},
  Number          = {3},
  Pages           = {270--284},
  Volume          = {255}
}

@Article{jiang2015a,
  Author          = {Jiang, Weiwei and Wu, Na and Wang, Xuemei and Chi,
                    Yujing and Zhang, Yuanyuan and Qiu, Xinyun and Hu, Ying
                    and Li, Jing and Liu, Yulan},
  Title           = {Dysbiosis gut microbiota associated with inflammation
                    and impaired mucosal immune function in intestine of
                    humans with non-alcoholic fatty liver disease},
  JournalTitle    = {Sci. Rep.},
  Date            = {2015},
  DOI             = {10.1038/srep08096},
  Number          = {1},
  Volume          = {5}
}

@Article{jordan2019a,
  Author          = {Jordan, Stefan and Tung, Navpreet and Casanova-Acebes,
                    Maria and Chang, Christie and Cantoni, Claudia and Zhang,
                    Dachuan and Wirtz, Theresa H. and Naik, Shruti and Rose,
                    Samuel A. and Brocker, Chad N. and Gainullina, Anastasiia
                    and Hornburg, Daniel and Horng, Sam and Maier, Barbara B.
                    and Cravedi, Paolo and LeRoith, Derek and Gonzalez, Frank
                    J. and Meissner, Felix and Ochando, Jordi and Rahman,
                    Adeeb and Chipuk, Jerry E. and Artyomov, Maxim N. and
                    Frenette, Paul S. and Piccio, Laura and Berres,
                    Marie-Luise and Gallagher, Emily J. and Merad, Miriam},
  Title           = {Dietary Intake Regulates the Circulating Inflammatory
                    Monocyte Pool},
  JournalTitle    = {Cell},
  Date            = {2019},
  DOI             = {10.1016/j.cell.2019.07.050},
  Addendum        = preliminarywork,
  ids             = {Jordan2019-pw},
  Keywords        = {Wirtz-Selection,Berres-Selection},
  Number          = {5},
  Pages           = {1102--1114.e17},
  Volume          = {178}
}

@Article{kalambokis2012a,
  Author          = {Kalambokis, Georgios N. and Tsianos, Epameinondas V.},
  Title           = {Rifaximin reduces endotoxemia and improves liver
                    function and disease severity in patients with
                    decompensated cirrhosis},
  JournalTitle    = {Hepatology},
  Date            = {2012},
  DOI             = {10.1002/hep.24751},
  Number          = {2},
  Pages           = {655--656},
  Volume          = {55}
}

@Article{karlson_effects_2017,
  Author          = {Karlson, Björn W. and Palmer, Michael K. and Nicholls,
                    Stephen J. and Barter, Philip J. and Lundman, Pia},
  Title           = {Effects of age, gender and statin dose on lipid levels:
                    {Results} from the {VOYAGER} meta-analysis database},
  JournalTitle    = {Atherosclerosis},
  Date            = {2017},
  DOI             = {10.1016/j.atherosclerosis.2017.08.014},
  Pages           = {54--59},
  ShortTitle      = {Effects of age, gender and statin dose on lipid levels},
  URLDate         = {2022-08-25},
  Volume          = {265}
}

@Article{keller2021a,
  Author          = {Keller, Josbert J. and Ooijevaar, Rogier E. and Hvas,
                    Christian L. and Terveer, Elisabeth M. and Lieberknecht,
                    Simone C. and Högenauer, Christoph and Arkkila, Perttu
                    and Sokol, Harry and Gridnyev, Oleksiy and Mégraud,
                    Francis and Kump, Patrizia K. and Nakov, Radislav and
                    Goldenberg, Simon D. and Satokari, Reetta and Tkatch,
                    Sergiy and Sanguinetti, Maurizio and Cammarota, Giovanni
                    and Dorofeev, Andrey and Gubska, Olena and Laniro,
                    Gianluca and Mattila, Eero and Arasaradnam, Ramesh P. and
                    Sarin, Shiv K. and Sood, Ajit and Putignani, Lorenza and
                    Alric, Laurent and Baunwall, Simon M. D. and Kupcinskas,
                    Juozas and Link, Alexander and Goorhuis, Abraham G. and
                    Verspaget, Hein W. and Ponsioen, Cyriel and Hold,
                    Georgina L. and Tilg, Herbert and Kassam, Zain and
                    Kuijper, Ed J. and Gasbarrini, Antonio and Mulder, Chris
                    J. J. and Williams, Horace R. T. and Vehreschild, Maria
                    J. G. T.},
  Title           = {A standardised model for stool banking for faecal
                    microbiota transplantation: {A} consensus report from a
                    multidisciplinary {UEG} working group},
  JournalTitle    = {United European Gastroenterol. J.},
  Date            = {2021},
  DOI             = {10.1177/2050640620967898},
  Keywords        = {Vehreschild-Selection},
  Number          = {2},
  Pages           = {229--247},
  Volume          = {9}
}

@Article{kim2019a,
  Author          = {Kim, S.J. and Feng, D. and Guillot, A. and Dai, S. and
                    Liu, F. and Hwang, S. and Parker, R. and Seo, W. and He,
                    Y. and Godlewski, G. and Jeong, W.I. and Lin, Y. and Qin,
                    X. and Kunos, G. and Gao, B.},
  Title           = {Adipocyte Death Preferentially Induces Liver Injury and
                    Inflammation Through the Activation of Chemokine {(C}-C
                    Motif) Receptor 2-Positive Macrophages and Lipolysis},
  JournalTitle    = {Hepatology},
  Date            = {2019},
  DOI             = {10.1002/hep.30525},
  Keywords        = {Guillot-Selection},
  Pages           = {1965--1982},
  Volume          = {69}
}

@Article{konig2017a,
  Author          = {König, J. and Siebenhaar, A. and Högenauer, C. and
                    Arkkila, P. and Nieuwdorp, M. and Norén, T. and
                    Ponsioen, C. Y. and Rosien, U. and Rossen, N. G. and
                    Satokari, R. and Stallmach, A. and de Vos, W. and Keller,
                    J. and Brummer, R. J.},
  Title           = {Consensus report: {Faecal} microbiota transfer -
                    clinical applications and procedures},
  JournalTitle    = {Aliment. Pharmacol. Ther.},
  Date            = {2016},
  DOI             = {10.1111/apt.13868},
  Number          = {2},
  Pages           = {222--239},
  Volume          = {45}
}

@Article{krauss2012a,
  Author          = {Krauss, Markus and Schaller, Stephan and Borchers,
                    Steffen and Findeisen, Rolf and Lippert, Jörg and
                    Kuepfer, Lars},
  Title           = {Integrating Cellular Metabolism into a Multiscale
                    Whole-Body Model},
  JournalTitle    = {PLoS Comput. Biol.},
  Date            = {2012},
  DOI             = {10.1371/journal.pcbi.1002750},
  Issue           = {8},
  Keywords        = {Küpfer-Selection},
  Number          = {10},
  Pages           = {e1002750},
  Volume          = {8}
}

@Article{kuepfer2016a,
  Author          = {Kuepfer, L and Niederalt, C and Wendl, T and Schlender,
                    J‐F and Willmann, S and Lippert, J and Block, M and
                    Eissing, T and Teutonico, D},
  Title           = {Applied Concepts in {PBPK} Modeling: {How} to Build a
                    {PBPK/PD} Model},
  JournalTitle    = {CPT: Pharmacomet. Syst. Pharmacol.},
  Date            = {2016},
  DOI             = {10.1002/psp4.12134},
  Keywords        = {Küpfer-Selection},
  Number          = {10},
  Pages           = {516--531},
  Volume          = {5}
}

@Article{kuhl2010a,
  Author          = {Kuhl, Christiane and Weigel, Stefanie and Schrading,
                    Simone and Arand, Birke and Bieling, Heribert and König,
                    Roy and Tombach, Bernd and Leutner, Claudia and
                    Rieber-Brambs, Andrea and Nordhoff, Dennis and Heindel,
                    Walter and Reiser, Maximilian and Schild, Hans H.},
  Title           = {Prospective Multicenter Cohort Study to Refine
                    Management Recommendations for Women at Elevated Familial
                    Risk of Breast Cancer: {The} {EVA} Trial},
  JournalTitle    = {J. Clin. Oncol.},
  Date            = {2010},
  DOI             = {10.1200/jco.2009.23.0839},
  Number          = {9},
  Pages           = {1450--1457},
  Volume          = {28}
}

@Article{kuhl2020,
  Author          = {Kuhl, Christiane K. and Lehman, Constance and Bedrosian,
                    Isabelle},
  Title           = {Imaging in Locoregional Management of Breast Cancer},
  JournalTitle    = {J. Clin. Oncol.},
  Date            = {2020},
  DOI             = {10.1200/jco.19.03257},
  Keywords        = {Kuhl-Selection},
  Number          = {20},
  Pages           = {2351--2361},
  PubState        = {accepted},
  Volume          = {38}
}

@Article{kummen2017a,
  Author          = {Kummen, Martin and Holm, Kristian and Anmarkrud, Jarl
                    Andreas and Nygård, Ståle and Vesterhus, Mette and
                    Høivik, Marte L and Trøseid, Marius and Marschall,
                    Hanns-Ulrich and Schrumpf, Erik and Moum, Bjørn and
                    Røsjø, Helge and Aukrust, Pål and Karlsen, Tom H and
                    Hov, Johannes R},
  Title           = {The gut microbial profile in patients with primary
                    sclerosing cholangitis is distinct from patients with
                    ulcerative colitis without biliary disease and healthy
                    controls},
  JournalTitle    = {Gut},
  Date            = {2016},
  DOI             = {10.1136/gutjnl-2015-310500},
  Number          = {4},
  Pages           = {611--619},
  Volume          = {66}
}

@Article{kuo2021a,
  Author          = {Kuo, Wei-Ting and Zuo, Li and Odenwald, Matthew A. and
                    Madha, Shariq and Singh, Gurminder and Gurniak, Christine
                    B. and Abraham, Clara and Turner, Jerrold R.},
  Title           = {The Tight Junction Protein {ZO}-1 Is Dispensable for
                    Barrier Function but Critical for Effective Mucosal
                    Repair},
  JournalTitle    = {Gastroenterology},
  Date            = {2021},
  DOI             = {10.1053/j.gastro.2021.08.047},
  Number          = {6},
  Pages           = {1924--1939},
  Volume          = {161}
}

@Article{kuttkat2017a,
  Author          = {Kuttkat, Nadine and Mohs, Antje and Ohl, Kim and
                    Hooiveld, Guido and Longerich, Thomas and Tenbrock, Klaus
                    and Cubero, Francisco Javier and Trautwein, Christian},
  Title           = {Hepatic overexpression of {cAMP}-responsive element
                    modulator α induces a regulatory T-cell response in a
                    murine model of chronic liver disease},
  JournalTitle    = {Gut},
  Date            = {2016},
  Addendum        = equal,
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1136/gutjnl-2015-311119},
  ids             = {Kuttkat:682566},
  Keywords        = {Mohs-Selection},
  Number          = {5},
  Pages           = {908--919},
  Volume          = {66}
}

@Article{lagkouvardos2016a,
  Author          = {Lagkouvardos, I. and Pukall, R. and Abt, B. and Foesel,
                    B.U. and Meier-Kolthoff, J.P. and Kumar, N. and
                    Bresciani, A. and Martinez, I. and Just, S. and Ziegler,
                    C. and Brugiroux, S. and Garzetti, D. and Wenning, M. and
                    Bui, T.P. and Wang, J. and Hugenholtz, F. and Plugge,
                    C.M. and Peterson, D.A. and Hornef, M.W. and Baines, J.F.
                    and Smidt, H. and Walter, J. and Kristiansen, K. and
                    Nielsen, H.B. and Haller, D. and Overmann, J. and
                    Stecher, B. and Clavel, T.},
  Title           = {The Mouse Intestinal Bacterial Collection {(miBC)}
                    provides host-specific insight into cultured diversity
                    and functional potential of the gut microbiota. {Nat}
                    Microbiol 1:16131.},
  Date            = {2016},
  DOI             = {10.1038/nmicrobiol.2016.131}
}

@Article{liao2019a,
  Author          = {Liao, Lijun and Schneider, Kai Markus and Galvez, Eric J
                    C and Frissen, Mick and Marschall, Hanns-Ulrich and Su,
                    Huan and Hatting, Maximilian and Wahlström, Annika and
                    Haybaeck, Johannes and Puchas, Philip and Mohs, Antje and
                    Peng, Jin and Bergheim, Ina and Nier, Anika and Hennings,
                    Julia and Reißing, Johanna and Zimmermann, Henning W and
                    Longerich, Thomas and Strowig, Till and Liedtke,
                    Christian and Cubero, Francisco J and Trautwein,
                    Christian},
  Title           = {Intestinal dysbiosis augments liver disease progression
                    via {NLRP3} in a murine model of primary sclerosing
                    cholangitis},
  JournalTitle    = {Gut},
  Addendum        = equal,
  Date            = {2019},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1136/gutjnl-2018-316670},
  Keywords        = {Mohs-Selection,SchneiderKM-Selection,Trautwein-Selection},
  Number          = {8},
  Pages           = {1477--1492},
  Volume          = {68}
}

@Article{Peter2013-tj,
  Author          = {Peter, Jack and Frey, Oliver and Stallmach, Andreas and
                    Bruns, Tony},
  Title           = {Attenuated antigen-specific T cell responses in
                    cirrhosis are accompanied by elevated serum
                    interleukin-10 levels and down-regulation of {HLA}-{DR}
                    on monocytes},
  JournalTitle    = {BMC Gastroenterol.},
  Date            = {2013},
  DOI             = {10.1186/1471-230x-13-37},
  Number          = {1},
  Pages           = {37},
  Volume          = {13}
}

@Article{Koch2014-uw,
  Author          = {Koch, Alexander and Zimmermann, Henning W. and Gassler,
                    Nikolaus and Jochum, Christoph and Weiskirchen, Ralf and
                    Bruensing, Jan and Buendgens, Lukas and Dückers, Hanna
                    and Bruns, Tony and Gerken, Guido and Neumann, Ulf P. and
                    Adams, David H. and Trautwein, Christian and Canbay, Ali
                    and Tacke, Frank},
  Title           = {Clinical relevance and cellular source of elevated
                    soluble urokinase plasminogen activator receptor
                    {(suPAR)} in acute liver failure},
  JournalTitle    = {Liver Int.},
  Date            = {2014},
  DOI             = {10.1111/liv.12512},
  Number          = {9},
  Pages           = {1330--1339},
  Volume          = {34}
}

@Article{Bruns2011-ts,
  Author          = {Bruns, T and Peter, J and Hagel, S and Herrmann, A and
                    Stallmach, A},
  Title           = {The augmented neutrophil respiratory burst in response
                    to \emph{Escherichia coli} is reduced in liver cirrhosis
                    during infection},
  JournalTitle    = {Clin. Exp. Immunol.},
  Date            = {2011},
  DOI             = {10.1111/j.1365-2249.2011.04373.x},
  Number          = {3},
  Pages           = {346--356},
  Volume          = {164}
}

@Article{lim2014a,
  Author          = {Lim, Chee Han and Voedisch, Sabrina and Wahl, Benjamin
                    and Rouf, Syed Fazle and Geffers, Robert and Rhen, Mikael
                    and Pabst, Oliver},
  Title           = {Independent Bottlenecks Characterize Colonization of
                    Systemic Compartments and Gut Lymphoid Tissue by
                    Salmonella},
  JournalTitle    = {PLoS Pathog.},
  Date            = {2014},
  DOI             = {10.1371/journal.ppat.1004270},
  Number          = {7},
  Pages           = {e1004270},
  Volume          = {10}
}

@Article{lindeman2021a,
  Author          = {Lindeman, Ida and Zhou, Chunyan and Eggesbø, Linn M.
                    and Miao, Zhichao and Polak, Justyna and Lundin, Knut
                    E.A. and Jahnsen, Jørgen and Qiao, Shuo-Wang and
                    Iversen, Rasmus and Sollid, Ludvig M.},
  Title           = {Longevity, clonal relationship, and transcriptional
                    program of celiac disease–specific plasma cells},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2021},
  DOI             = {10.1084/jem.20200852},
  Number          = {2},
  Volume          = {218}
}

@Article{Llovet2022-jd,
  Author          = {Llovet, Josep M. and Pinyol, Roser and Kelley, Robin K.
                    and El-Khoueiry, Anthony and Reeves, Helen L. and Wang,
                    Xin Wei and Gores, Gregory J. and Villanueva, Augusto},
  Title           = {Molecular pathogenesis and systemic therapies for
                    hepatocellular carcinoma},
  JournalTitle    = {Nat. Cancer.},
  Date            = {2022},
  DOI             = {10.1038/s43018-022-00357-2},
  Number          = {4},
  Pages           = {386--401},
  Volume          = {3}
}

@Article{llopis2016a,
  Author          = {Llopis, M and Cassard, A M and Wrzosek, L and Boschat, L
                    and Bruneau, A and Ferrere, G and Puchois, V and Martin,
                    J C and Lepage, P and Le Roy, T and Lefèvre, L and
                    Langelier, B and Cailleux, F and González-Castro, A M
                    and Rabot, S and Gaudin, F and Agostini, H and Prévot, S
                    and Berrebi, D and Ciocan, D and Jousse, C and Naveau, S
                    and Gérard, P and Perlemuter, G},
  Title           = {Intestinal microbiota contributes to individual
                    susceptibility to alcoholic liver disease},
  JournalTitle    = {Gut},
  Date            = {2015},
  DOI             = {10.1136/gutjnl-2015-310585},
  Number          = {5},
  Pages           = {830--839},
  Volume          = {65}
}

@Article{lupar2015a,
  Author          = {Lupar, Ekaterina and Brack, Maria and Garnier, Laure and
                    Laffont, Sophie and Rauch, Katharina S. and Schachtrup,
                    Kristina and Arnold, Sebastian J. and Guéry,
                    Jean-Charles and Izcue, Ana},
  Title           = {Eomesodermin Expression in CD4\textsuperscript{+} T
                    Cells Restricts Peripheral Foxp3 Induction},
  JournalTitle    = {J. Immunol.},
  Date            = {2015},
  DOI             = {10.4049/jimmunol.1501159},
  Keywords        = {Izcue-Selection},
  Number          = {10},
  Pages           = {4742--4752},
  Volume          = {195}
}

@Article{macpherson2009a,
  Author          = {Macpherson, Andrew J. and Slack, Emma and Geuking,
                    Markus B. and McCoy, Kathy D.},
  Title           = {The mucosal firewalls against commensal intestinal
                    microbes},
  JournalTitle    = {Semin. Immunopathol.},
  Date            = {2009},
  DOI             = {10.1007/s00281-009-0174-3},
  Number          = {2},
  Pages           = {145--149},
  Volume          = {31}
}

@Article{manning1984a,
  Author          = {Manning, Ronald J. and Walker, Patricia G. and Carter,
                    Lisa and Barrington, Patricia J. and Jackson, Graham
                    D.F.},
  Title           = {Studies on the origins of biliary immunoglobulins in
                    rats},
  JournalTitle    = {Gastroenterology},
  Date            = {1984},
  DOI             = {10.1016/0016-5085(84)90141-0},
  Number          = {1},
  Pages           = {173--179},
  Volume          = {87}
}

@Article{marchesi2016a,
  Author          = {Marchesi, Julian R and Adams, David H and Fava,
                    Francesca and Hermes, Gerben D A and Hirschfield, Gideon
                    M and Hold, Georgina and Quraishi, Mohammed Nabil and
                    Kinross, James and Smidt, Hauke and Tuohy, Kieran M and
                    Thomas, Linda V and Zoetendal, Erwin G and Hart, Ailsa},
  Title           = {The gut microbiota and host health: {A} new clinical
                    frontier},
  JournalTitle    = {Gut},
  Date            = {2015},
  DOI             = {10.1136/gutjnl-2015-309990},
  Number          = {2},
  Pages           = {330--339},
  Volume          = {65}
}

@Article{mas2003a,
  Author          = {Mas, Antoni and Rodés, Juan and Sunyer, Lourdes and
                    Rodrigo, Luı́s and Planas, Ramon and Vargas, Victor and
                    Castells, Lluı́s and Rodrı́guez-Martı́nez, Dolores
                    and Fernández-Rodrı́guez, Conrado and Coll, Ignasi and
                    Pardo, Albert},
  Title           = {Comparison of rifaximin and lactitol in the treatment of
                    acute hepatic encephalopathy: {Results} of a randomized,
                    double-blind, double-dummy, controlled clinical trial},
  JournalTitle    = {J. Hepatol.},
  Date            = {2003},
  DOI             = {10.1016/s0168-8278(02)00350-1},
  Number          = {1},
  Pages           = {51--58},
  Volume          = {38}
}

@Article{mayer_implementing_2021,
  Author          = {Mayer, Gerhard and others},
  Title           = {Implementing {FAIR} data management within the German
                    Network for Bioinformatics Infrastructure (de.{NBI})
                    exemplified by selected use cases},
  JournalTitle    = {Brief. Bioinform.},
  Date            = {2021-09-02},
  DOI             = {10.1093/bib/bbab010},
  Keywords        = {Bioinformatics,{FAIR} practice,{SOP},implementation},
  langid          = {english},
  Number          = {5},
  Pages           = {bbab010},
  URLDate         = {2022-04-05},
  Volume          = {22}
}

@Article{meinicke2017a,
  Author          = {Meinicke, Holger and Bremser, Anna and Brack, Maria and
                    Akeus, Paulina and Pearson, Claire and Bullers, Samuel
                    and Hoffmeyer, Katrin and Stemmler, Marc P. and
                    Quiding-Järbrink, Marianne and Izcue, Ana},
  Title           = {Tumour-associated changes in intestinal epithelial cells
                    cause local accumulation of {KLRG1\textsuperscript{+}}
                    {GATA3\textsuperscript{+}} regulatory T cells in mice},
  JournalTitle    = {Immunology},
  Date            = {2017},
  DOI             = {10.1111/imm.12750},
  Keywords        = {Izcue-Selection},
  Number          = {1},
  Addendum        = preliminarywork,
  Pages           = {74--88},
  Volume          = {152}
}

@Article{meinicke2017b,
  Author          = {Meinicke, Holger and Bremser, Anna and Brack, Maria and
                    Schrenk, Klaudia and Pircher, Hanspeter and Izcue, Ana},
  Title           = {{KLRG1} impairs regulatory T-cell competitive fitness in
                    the gut},
  JournalTitle    = {Immunology},
  Date            = {2017},
  DOI             = {10.1111/imm.12749},
  Keywords        = {Izcue-Selection},
  Number          = {1},
  Pages           = {65--73},
  Volume          = {152}
}

@Article{mierlo2016a,
  Author          = {van Mierlo, Kim M.C. and Schaap, Frank G. and Dejong,
                    Cornelis H.C. and Olde Damink, Steven W.M.},
  Title           = {Liver resection for cancer: {New} developments in
                    prediction, prevention and management of postresectional
                    liver failure},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2016.06.006},
  Keywords        = {Schaap-Selection},
  Number          = {6},
  Pages           = {1217--1231},
  Volume          = {65}
}

@Article{mohs2017a,
  Author          = {Mohs, Antje and Kuttkat, Nadine and Reißing, Johanna
                    and Zimmermann, Henning Wolfgang and Sonntag, Roland and
                    Proudfoot, Amanda and Youssef, Sameh A. and de Bruin,
                    Alain and Cubero, Francisco Javier and Trautwein,
                    Christian},
  Title           = {Functional role of {CCL5/RANTES} for {HCC} progression
                    during chronic liver disease},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  author+an:default = {10=sharedLast;9=sharedLast},
  DOI             = {10.1016/j.jhep.2016.12.011},
  Keywords        = {Mohs-Selection},
  Number          = {4},
  Addendum        = sharedlast,
  Pages           = {743--753},
  Volume          = {66}
}

@Article{mohs2020a,
  Author          = {Mohs, Antje and Otto, Tobias and Schneider, Kai Markus
                    and Peltzer, Mona and Boekschoten, Mark and Holland,
                    Christian H. and Hudert, Christian A. and Kalveram, Laura
                    and Wiegand, Susanna and Saez-Rodriguez, Julio and
                    Longerich, Thomas and Hengstler, Jan G. and Trautwein,
                    Christian},
  Title           = {Hepatocyte-specific {NRF2} activation controls
                    fibrogenesis and carcinogenesis in steatohepatitis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2021},
  DOI             = {10.1016/j.jhep.2020.09.037},
  Keywords        = {Mohs-Selection,Trautwein-Selection},
  Number          = {3},
  Pages           = {638--648},
  Volume          = {74}
}

@Article{mohs2020b,
  Author          = {Mohs, Antje and Kuttkat, Nadine and Otto, Tobias and
                    Youssef, Sameh A and De Bruin, Alain and Trautwein,
                    Christian},
  Title           = {{MyD88}-dependent signaling in non-parenchymal cells
                    promotes liver carcinogenesis},
  JournalTitle    = {Carcinogenesis},
  Date            = {2019},
  Addendum        = equal,
  author+an:default = {1=equal;2=equal;3=equal},
  DOI             = {10.1093/carcin/bgy173},
  Keywords        = {Mohs-Selection},
  Number          = {2},
  Pages           = {171--181},
  Volume          = {41}
}

@Article{moor2017a,
  Author          = {Moor, Kathrin and Diard, Médéric and Sellin, Mikael E.
                    and Felmy, Boas and Wotzka, Sandra Y. and Toska, Albulena
                    and Bakkeren, Erik and Arnoldini, Markus and Bansept,
                    Florence and Co, Alma Dal and Völler, Tom and Minola,
                    Andrea and Fernandez-Rodriguez, Blanca and Agatic, Gloria
                    and Barbieri, Sonia and Piccoli, Luca and Casiraghi,
                    Costanza and Corti, Davide and Lanzavecchia, Antonio and
                    Regoes, Roland R. and Loverdo, Claude and Stocker, Roman
                    and Brumley, Douglas R. and Hardt, Wolf-Dietrich and
                    Slack, Emma},
  Title           = {High-avidity {IgA} protects the intestine by enchaining
                    growing bacteria},
  JournalTitle    = {Nature},
  Date            = {2017},
  DOI             = {10.1038/nature22058},
  Number          = {7651},
  Pages           = {498--502},
  Volume          = {544}
}

@Article{moro-sibilot2016a,
  Author          = {Moro-Sibilot, Ludovic and Blanc, Pascal and Taillardet,
                    Morgan and Bardel, Emilie and Couillault, Coline and
                    Boschetti, Gilles and Traverse-Glehen, Alexandra and
                    Defrance, Thierry and Kaiserlian, Dominique and Dubois,
                    Bertrand},
  Title           = {Mouse and Human Liver Contain Immunoglobulin
                    {A–Secreting} Cells Originating From Peyer's Patches
                    and Directed Against Intestinal Antigens},
  JournalTitle    = {Gastroenterology},
  Date            = {2016},
  DOI             = {10.1053/j.gastro.2016.04.014},
  Number          = {2},
  Pages           = {311--323},
  Volume          = {151}
}

@Article{Mousa2021-ov,
  Author          = {Mousa, Omar Y. and Juran, Brian D. and McCauley, Bryan
                    M. and Vesterhus, Mette N. and Folseraas, Trine and
                    Turgeon, Coleman T. and Ali, Ahmad H. and Schlicht, Erik
                    M. and Atkinson, Elizabeth J. and Hu, Chang and Harnois,
                    Denise and Carey, Elizabeth J. and Gossard, Andrea A. and
                    Oglesbee, Devin and Eaton, John E. and LaRusso, Nicholas
                    F. and Gores, Gregory J. and Karlsen, Tom H. and
                    Lazaridis, Konstantinos N.},
  Title           = {Bile Acid Profiles in Primary Sclerosing Cholangitis and
                    Their Ability to Predict Hepatic Decompensation},
  JournalTitle    = {Hepatology},
  Date            = {2021},
  DOI             = {10.1002/hep.31652},
  Number          = {1},
  Pages           = {281--295},
  Volume          = {74}
}

@Article{mouzaki2013a,
  Author          = {Mouzaki, Marialena and Comelli, Elena M. and Arendt,
                    Bianca M. and Bonengel, Julia and Fung, Scott K. and
                    Fischer, Sandra E. and McGilvray, Ian D. and Allard,
                    Johane P.},
  Title           = {Intestinal microbiota in patients with nonalcoholic
                    fatty liver disease},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26319},
  Number          = {1},
  Pages           = {120--127},
  Volume          = {58}
}

@Article{mowat2014a,
  Author          = {Mowat, Allan M. and Agace, William W.},
  Title           = {Regional specialization within the intestinal immune
                    system},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2014},
  DOI             = {10.1038/nri3738},
  Number          = {10},
  Pages           = {667--685},
  Volume          = {14}
}

@InProceedings{muller-newen2018a,
  Author          = {Muller-Newen, G. and Abdallah, A.T. and Weiskirchen, R.
                    and Ticconi, F. and Costa, I.G. and Barbacid, M. and
                    Trautwein, C. and Liedtke, C.},
  Title           = {Cyclin E1 and cyclin-dependent kinase 2 are critical for
                    initiation, but not for progression of hepatocellular
                    carcinoma},
  Date            = {2018},
  BookTitle       = {Proceedings of the National Academy of Sciences of the
                    United States of America 115:9282-9287}
}

@Article{nagao-kitamoto2017a,
  Author          = {Nagao-Kitamoto, Hiroko and Kamada, Nobuhiko},
  Title           = {Host-microbial Cross-talk in Inflammatory Bowel
                    Disease},
  JournalTitle    = {Immune Netw.rk},
  Date            = {2017},
  DOI             = {10.4110/in.2017.17.1.1},
  Number          = {1},
  Pages           = {1},
  Volume          = {17}
}

@Article{Hosp2017-na,
  Author          = {Hosp, Fabian and Gutiérrez-Ángel, Sara and Schaefer,
                    Martin H. and Cox, Jürgen and Meissner, Felix and Hipp,
                    Mark S. and Hartl, F.-Ulrich and Klein, Rüdiger and
                    Dudanova, Irina and Mann, Matthias},
  Title           = {Spatiotemporal Proteomic Profiling of {Huntington’s}
                    Disease Inclusions Reveals Widespread Loss of Protein
                    Function},
  JournalTitle    = {Cell Rep.},
  Date            = {2017},
  DOI             = {10.1016/j.celrep.2017.10.097},
  Number          = {8},
  Pages           = {2291--2303},
  Volume          = {21}
}

@Article{nagura1983a,
  Author          = {Nagura, H. and Tsutsumi, Y. and Hasegawa, H. and
                    Watanabe, K. and Nakane, P.K. and Brown, W.R.},
  Title           = {{IgA} plasma cells in biliary mucosa: {A} likely source
                    of locally synthesized {IgA} in human hepatic bile},
  JournalTitle    = {Clin. Exp. Immunol.},
  Date            = {1983},
  Pages           = {671--680},
  Volume          = {54}
}

@Article{neemann2017a,
  Author          = {Neemann, Kari and Freifeld, Alison},
  Title           = {Clostridium {difficile–Associated} Diarrhea in the
                    Oncology Patient},
  JournalTitle    = {J. Oncol. Pract.},
  Date            = {2017},
  DOI             = {10.1200/jop.2016.018614},
  Number          = {1},
  Pages           = {25--30},
  Volume          = {13}
}

@Article{neis2018a,
  Author          = {Neis, Evelien PJG and van Eijk, Hans MH and Lenaerts,
                    Kaatje and Olde Damink, Steven WM and Blaak, Ellen E and
                    Dejong, Cornelis HC and Rensen, Sander S},
  Title           = {Distal versus proximal intestinal short-chain fatty acid
                    release in man},
  JournalTitle    = {Gut},
  Date            = {2018},
  DOI             = {10.1136/gutjnl-2018-316161},
  Number          = {4},
  Pages           = {764--765},
  Volume          = {68}
}

@Article{neufert2021a,
  Author          = {Neufert, Clemens and Heichler, Christina and Brabletz,
                    Thomas and Scheibe, Kristina and Boonsanay, Verawan and
                    Greten, Florian R. and Neurath, Markus F.},
  Title           = {Inducible mouse models of colon cancer for the analysis
                    of sporadic and inflammation-driven tumor progression and
                    lymph node metastasis},
  JournalTitle    = {Nat. Protoc.},
  Date            = {2020},
  DOI             = {10.1038/s41596-020-00412-1},
  Number          = {1},
  Pages           = {61--85},
  Volume          = {16}
}

@Article{pabst2004a,
  Author          = {Pabst, Oliver and Ohl, Lars and Wendland, Meike and
                    Wurbel, Marc-André and Kremmer, Elisabeth and Malissen,
                    Bernard and Förster, Reinhold},
  Title           = {Chemokine Receptor {CCR9} Contributes to the
                    Localization of Plasma Cells to the Small Intestine},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2004},
  DOI             = {10.1084/jem.20030996},
  Number          = {3},
  Pages           = {411--416},
  Volume          = {199}
}

@Article{pabst2006a,
  Author          = {Pabst, Oliver and Herbrand, Heike and Friedrichsen,
                    Michaela and Velaga, Sarvari and Dorsch, Martina and
                    Berhardt, Günter and Worbs, Tim and Macpherson, Andrew
                    J. and Förster, Reinhold},
  Title           = {Adaptation of Solitary Intestinal Lymphoid Tissue in
                    Response to Microbiota and Chemokine Receptor {CCR7}
                    Signaling},
  JournalTitle    = {J. Immunol.},
  Date            = {2006},
  DOI             = {10.4049/jimmunol.177.10.6824},
  Number          = {10},
  Pages           = {6824--6832},
  Volume          = {177}
}

@Article{pabst2012a,
  Author          = {Pabst, Oliver},
  Title           = {New concepts in the generation and functions of {IgA}},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2012},
  DOI             = {10.1038/nri3322},
  Number          = {12},
  Pages           = {821--832},
  Volume          = {12}
}

@Article{pabst2013a,
  Author          = {Pabst, O. and Paramsothy, S. and Kamm, M.A. and
                    Kaakoush, N.O. and Walsh, A.J. and Bogaerde, J. and
                    Samuel, D. and Leong, R.W. and Connor, S. and Ng, W. and
                    R.},
  Title           = {Trafficking of regulatory T cells in the intestinal
                    immune system},
  JournalTitle    = {Int. Immunol.},
  Date            = {2013},
  DOI             = {10.1093/intimm/dxs113},
  Pages           = {139--143},
  Volume          = {25}
}

@Article{pabst2016a,
  Author          = {Pabst, Oliver and Cerovic, Vuk and Hornef, Mathias},
  Title           = {Secretory {IgA} in the Coordination of Establishment and
                    Maintenance of the Microbiota},
  JournalTitle    = {Trends Immunol.},
  Date            = {2016},
  DOI             = {10.1016/j.it.2016.03.002},
  Keywords        = {Peer-B06},
  Number          = {5},
  Pages           = {287--296},
  Volume          = {37}
}

@Article{paramsothy2017a,
  Author          = {Paramsothy, Sudarshan and Kamm, Michael A and Kaakoush,
                    Nadeem O and Walsh, Alissa J and van den Bogaerde, Johan
                    and Samuel, Douglas and Leong, Rupert W L and Connor,
                    Susan and Ng, Watson and Paramsothy, Ramesh and Xuan, Wei
                    and Lin, Enmoore and Mitchell, Hazel M and Borody, Thomas
                    J},
  Title           = {Multidonor intensive faecal microbiota transplantation
                    for active ulcerative colitis: {A} randomised
                    placebo-controlled trial},
  JournalTitle    = {The Lancet},
  Date            = {2017},
  DOI             = {10.1016/s0140-6736(17)30182-4},
  Number          = {10075},
  Pages           = {1218--1228},
  Volume          = {389}
}

@Article{vanMierlo2022-ok,
  Author          = {van Mierlo, Kim M.C and Dahrenmoller, Carola and Lebrun,
                    Valerie and Jansen, Peter L.M. and Dejong, Cornelis H.C.
                    and Leclercq, Isabelle A. and Olde Damink, Steven W. M.
                    and Schaap, Frank G.},
  Title           = {The {FXR} agonist obeticholic acid does not stimulate
                    liver regeneration in hepatectomized mice},
  Date            = {2022},
  DOI             = {10.1101/2022.11.10.515905}
}

@Article{vanMierlo2022-df,
  Author          = {van Mierlo, Kim M.C and van Himbeeck, Cathy and Lebrun,
                    Valerie and Jansen, Peter L.M. and Dejong, Cornelius H.C.
                    and Leclercq, Isabelle A. and Olde Damink, Steven W. M.
                    and Schaap, Frank G.},
  Title           = {Development of a mouse model for postresectional liver
                    failure.},
  Date            = {2022},
  DOI             = {10.1101/2022.11.10.515992}
}

@Article{pedersen2022,
  Author          = {Pedersen, Kristian Jensen and Haange, Sven-Bastiaan and
                    Žížalová, Kateřina and Viehof, Alina and Clavel,
                    Thomas and Leniček, Martin and Engelmann, Beatrice and
                    Wick, Lukas Y. and Schaap, Frank G. and Jehmlich, Nico
                    and Rolle-Kampczyk, Ulrike and von Bergen, Martin},
  Title           = {Eggerthella lenta {DSM} 2243 Alleviates Bile Acid Stress
                    Response in Clostridium ramosum and Anaerostipes caccae
                    by Transformation of Bile Acids},
  JournalTitle    = {Microorganisms},
  Date            = {2022},
  DOI             = {10.3390/microorganisms10102025},
  ids             = {Pedersen:854665},
  Keywords        = {,CRC1382-Project A05,CRC1382-Project Q02,CRC1382-Project
                    A07,CRC1382-Project A05,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {10},
  Pages           = {2025},
  Volume          = {10}
}

@Article{Baskaya2021-xv,
  Author          = {Baskaya, Feran and Lederle, Wiltrud and Kiessling,
                    Fabian},
  Title           = {Detection and differentiation of pathophysiological
                    changes in non-alcoholic steatohepatitis and inflammatory
                    liver fibrosis in mice by multiparametric {MRI.}
                    Proceedings of the world molecular imaging congress 2021,
                    {October} 5-8, 2021: {Abstract} No. 28},
  JournalTitle    = {Mol. Imaging Biol.},
  Date            = {2021},
  Number          = {Suppl 2},
  Volume          = {23}
}

@Misc{Schraven2022-abstractEMIM,
  Author          = {Schraven, Sarah and Rosenhain, Stefanie and Brück,
                    Ramona and Wiechmann, Tim and Pola, Robert and Etrych,
                    Thomas and Lederle, Wiltrud and Gremse, Felix and
                    Kiessling, Fabian},
  Title           = {Fluorescent dye labeling strongly influences tumor
                    accumulation and biodistribution of polymeric drug
                    carriers. {European} Molecular Imaging Meeting 2022:
                    {Abstract} 803},
  Date            = {2022}
}

@Article{pedersoli2020a,
  Author          = {Pedersoli, Federico and Zimmermann, Markus and
                    Schulze-Hagen, Maximilian and Sieben, Paul and Barzakova,
                    Emona and Goerg, Fabian and Keil, Sebastian and Gombert,
                    Alexander and Kuhl, Christiane K. and Isfort, Peter and
                    Bruners, Philipp},
  Title           = {Retrograde Recanalization of the Celiac Artery via the
                    Pancreaticoduodenal Arcade as a Safe and Valid
                    Alternative to Antegrade Access},
  JournalTitle    = {Vasc. Endovasc. Surg.},
  Date            = {2020},
  DOI             = {10.1177/1538574420927132},
  Keywords        = {Barzakova-Selection},
  Number          = {6},
  Pages           = {477--481},
  Volume          = {54}
}

@Article{pedersoli2022a,
  Author          = {Pedersoli, F. and Van den Bosch, V. and Sieben, P. and
                    Barzakova, E. and Schulze-Hagen, M. and Isfort, P. and
                    Keil, S. and Wiltberger, G. and Kuhl, C. K. and Bruners,
                    P.},
  Title           = {Stent Graft Placement by Pseudoaneurysm of the Hepatic
                    Arteries: {Efficacy} and Patency Rate in Follow-up},
  JournalTitle    = {CardioVasc. Interv. Radiol.},
  Date            = {2021},
  DOI             = {10.1007/s00270-021-02993-0},
  Keywords        = {Barzakova-Selection},
  Number          = {1},
  Pages           = {21--28},
  Volume          = {45}
}

@Article{peterson2015a,
  Author          = {Peterson, Daniel A. and Planer, Joseph D. and Guruge,
                    Janaki L. and Xue, Lai and Downey-Virgin, Whitt and
                    Goodman, Andrew L. and Seedorf, Henning and Gordon,
                    Jeffrey I.},
  Title           = {Characterizing the Interactions between a Naturally
                    Primed Immunoglobulin A and Its Conserved Bacteroides
                    thetaiotaomicron Species-specific Epitope in Gnotobiotic
                    Mice},
  JournalTitle    = {J. Biol. Chem.},
  Date            = {2015},
  DOI             = {10.1074/jbc.m114.633800},
  ids             = {Peterson2015Characterizing},
  Number          = {20},
  Pages           = {12630--12649},
  Volume          = {290}
}

@Article{pott2016a,
  Author          = {Pott, Johanna and Maloy, Kevin J and Izcue, Ana},
  Title           = {Barrier regulation: {Tolerance} stops at cell death},
  JournalTitle    = {Nat. Immunol.},
  Date            = {2016},
  DOI             = {10.1038/ni.3418},
  Keywords        = {Izcue-Selection},
  Number          = {4},
  Pages           = {349--350},
  Volume          = {17}
}

@Article{prasad2007a,
  Author          = {Prasad, Srinivasa and Dhiman, Radha K. and Duseja, Ajay
                    and Chawla, Yogesh K. and Sharma, Arpita and Agarwal,
                    Ritesh},
  Title           = {Lactulose improves cognitive functions and
                    health-related quality of life in patients with cirrhosis
                    who have minimal hepatic encephalopathy},
  JournalTitle    = {Hepatology},
  Date            = {2007},
  DOI             = {10.1002/hep.21533},
  Number          = {3},
  Pages           = {549--559},
  Volume          = {45}
}

@Article{qin2014a,
  Author          = {Qin, Nan and Yang, Fengling and Li, Ang and Prifti, Edi
                    and Chen, Yanfei and Shao, Li and Guo, Jing and Le
                    Chatelier, Emmanuelle and Yao, Jian and Wu, Lingjiao and
                    Zhou, Jiawei and Ni, Shujun and Liu, Lin and Pons,
                    Nicolas and Batto, Jean Michel and Kennedy, Sean P. and
                    Leonard, Pierre and Yuan, Chunhui and Ding, Wenchao and
                    Chen, Yuanting and Hu, Xinjun and Zheng, Beiwen and Qian,
                    Guirong and Xu, Wei and Ehrlich, S. Dusko and Zheng,
                    Shusen and Li, Lanjuan},
  Title           = {Alterations of the human gut microbiome in liver
                    cirrhosis},
  JournalTitle    = {Nature},
  Date            = {2014},
  DOI             = {10.1038/nature13568},
  Number          = {7516},
  Pages           = {59--64},
  Volume          = {513}
}

@Article{rausch2016a,
  Author          = {Rausch, Philipp and Basic, Marijana and Batra, Arvind
                    and Bischoff, Stephan C. and Blaut, Michael and Clavel,
                    Thomas and Gläsner, Joachim and Gopalakrishnan, Shreya
                    and Grassl, Guntram A. and Günther, Claudia and Haller,
                    Dirk and Hirose, Misa and Ibrahim, Saleh and Loh, Gunnar
                    and Mattner, Jochen and Nagel, Stefan and Pabst, Oliver
                    and Schmidt, Franziska and Siegmund, Britta and Strowig,
                    Till and Volynets, Valentina and Wirtz, Stefan and
                    Zeissig, Sebastian and Zeissig, Yvonne and Bleich, André
                    and Baines, John F.},
  Title           = {Analysis of factors contributing to variation in the
                    {C57BL/6J} fecal microbiota across {German} animal
                    facilities},
  JournalTitle    = {Int. J. Med. Microbiol.},
  Date            = {2016},
  DOI             = {10.1016/j.ijmm.2016.03.004},
  Number          = {5},
  Pages           = {343--355},
  Volume          = {306}
}

@Article{reissing2022a,
  Author          = {Reißing, Johanna and Lutz, Philipp and Frissen, Mick
                    and Ibidapo-Obe, Oluwatomi and Reuken, Philipp A. and
                    Wirtz, Theresa H. and Stengel, Sven and Quickert,
                    Stefanie and Rooney, Michael and Große, Karsten and
                    Zimmermann, Henning W. and Trautwein, Christian and
                    Stallmach, Andreas and Bruns, Tony},
  Title           = {Immunomodulatory receptor {VSIG4} is released during
                    spontaneous bacterial peritonitis and predicts short-term
                    mortality},
  JournalTitle    = {JHEP Reports},
  Date            = {2022},
  DOI             = {10.1016/j.jhepr.2021.100391},
  ids             = {Reising2022-mg},
  Keywords        = {Wirtz-Selection,Bruns-Selection},
  Number          = {1},
  Pages           = {100391},
  Volume          = {4}
}

@Article{rheinwalt_baseline_2020,
  Author          = {Rheinwalt, Karl Peter and Drebber, Uta and Schierwagen,
                    Robert and Klein, Sabine and Neumann, Ulf Peter and
                    Ulmer, Tom Florian and Plamper, Andreas and Kroh, Andreas
                    and Schipper, Sandra and Odenthal, Margarete and Uschner,
                    Frank Erhard and Lingohr, Philipp and Trebicka, Jonel and
                    Brol, Maximilian Joseph},
  Title           = {Baseline Presence of {NAFLD} Predicts Weight Loss after
                    Gastric Bypass Surgery for Morbid Obesity},
  JournalTitle    = {J. Clin. Med.},
  Date            = {2020},
  DOI             = {10.3390/jcm9113430},
  Number          = {11},
  Pages           = {3430},
  URLDate         = {2022-08-25},
  Volume          = {9}
}

@Article{rizvi2015a,
  Author          = {Rizvi, Sumera and Eaton, John E. and Gores, Gregory J.},
  Title           = {Primary Sclerosing Cholangitis as a Premalignant Biliary
                    Tract Disease: {Surveillance} and Management},
  JournalTitle    = {Clin. Gastroenterol. Hepatol.},
  Date            = {2015},
  DOI             = {10.1016/j.cgh.2015.05.035},
  Number          = {12},
  Pages           = {2152--2165},
  Volume          = {13}
}

@Article{roessner2021a,
  Author          = {Roessner, P.M. and Cid, L.Llao and Lupar, E. and Roider,
                    T. and Bordas, M. and Schifflers, C. and Arseni, L. and
                    Gaupel, A.C. and Kilpert, F. and Krotschel, M. and
                    Arnold, S.J. and Sellner, L. and Colomer, D. and
                    Stilgenbauer, S. and Dietrich, S. and Lichter, P. and
                    Izcue, A. and Seiffert, M.},
  Title           = {{EOMES} and {IL}-10 regulate antitumor activity of T
                    regulatory type 1 {CD4(+)} T cells in chronic lymphocytic
                    leukemia},
  JournalTitle    = {Leukemia},
  Date            = {2021},
  Addendum        = sharedlastpreliminarywork,
  author+an:default = {17=sharedLast;18=sharedLast},
  DOI             = {10.1038/s41375-021-01136-1},
  Keywords        = {Izcue-Selection},
  Pages           = {2311--2324},
  Volume          = {35}
}

@Article{Nakajima2018-wn,
  Author          = {Nakajima, Akira and Vogelzang, Alexis and Maruya, Mikako
                    and Miyajima, Michio and Murata, Megumi and Son, Aoi and
                    Kuwahara, Tomomi and Tsuruyama, Tatsuaki and Yamada,
                    Satoshi and Matsuura, Minoru and Nakase, Hiroshi and
                    Peterson, Daniel A. and Fagarasan, Sidonia and Suzuki,
                    Keiichiro},
  Title           = {{IgA} regulates the composition and metabolic function
                    of gut microbiota by promoting symbiosis between
                    bacteria},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2018},
  DOI             = {10.1084/jem.20180427},
  Number          = {8},
  Pages           = {2019--2034},
  Volume          = {215}
}

@Article{rollenske2021a,
  Author          = {Rollenske, Tim and Burkhalter, Sophie and Muerner, Lukas
                    and von Gunten, Stephan and Lukasiewicz, Jolanta and
                    Wardemann, Hedda and Macpherson, Andrew J.},
  Title           = {Parallelism of intestinal secretory {IgA} shapes
                    functional microbial fitness},
  JournalTitle    = {Nature},
  Date            = {2021},
  DOI             = {10.1038/s41586-021-03973-7},
  Number          = {7882},
  Pages           = {657--661},
  Volume          = {598}
}

@Article{ruhlemann2017a,
  Author          = {Rühlemann, Malte Christoph and Heinsen, Femke-Anouska
                    and Zenouzi, Roman and Lieb, Wolfgang and Franke, Andre
                    and Schramm, Christoph},
  Title           = {Faecal microbiota profiles as diagnostic biomarkers in
                    primary sclerosing cholangitis},
  JournalTitle    = {Gut},
  Date            = {2016},
  DOI             = {10.1136/gutjnl-2016-312180},
  Number          = {4},
  Pages           = {753--754},
  Volume          = {66}
}

@Article{sackett2019a,
  Author          = {Sackett, Sara Dutton and Otto, Tobias and Mohs, Antje
                    and Sander, Leif E. and Strauch, Sonja and Streetz,
                    Konrad L. and Kroy, Daniela C. and Trautwein, Christian},
  Title           = {Myeloid cells require gp130 signaling for protective
                    anti‐inflammatory functions during sepsis},
  JournalTitle    = {The FASEB Journal},
  Date            = {2019},
  author+an:default = {1=equal;2=equal},
  Addendum        = equal,
  DOI             = {10.1096/fj.201802118r},
  Keywords        = {Mohs-Selection},
  Note            = {*equal contribution},
  Number          = {5},
  Pages           = {6035--6044},
  Volume          = {33}
}

@Article{schenk2017a,
  Author          = {Schenk, Arne and Ghallab, Ahmed and Hofmann, Ute and
                    Hassan, Reham and Schwarz, Michael and Schuppert, Andreas
                    and Schwen, Lars Ole and Braeuning, Albert and Teutonico,
                    Donato and Hengstler, Jan G. and Kuepfer, Lars},
  Title           = {Physiologically-based modelling in mice suggests an
                    aggravated loss of clearance capacity after toxic liver
                    damage},
  JournalTitle    = {Sci. Rep.},
  Date            = {2017},
  DOI             = {10.1038/s41598-017-04574-z},
  Keywords        = {Küpfer-Selection},
  Number          = {1},
  Volume          = {7}
}

@Article{schierwagen_rationale_2017,
  Author          = {Schierwagen, Robert and Uschner, Frank Erhard and
                    Magdaleno, Fernando and Klein, Sabine and Trebicka,
                    Jonel},
  Title           = {Rationale for the use of statins in liver disease},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2017},
  DOI             = {10.1152/ajpgi.00441.2016},
  Keywords        = {Animals,Humans,Hydroxymethylglutaryl-CoA Reductase
                    Inhibitors,Liver Diseases},
  Number          = {5},
  Pages           = {G407--G412},
  Volume          = {312}
}

@Article{schierwagen_statins_2016,
  Author          = {Schierwagen, Robert and Maybüchen, Lara and Hittatiya,
                    Kanishka and Klein, Sabine and Uschner, Frank E. and
                    Braga, Tarcio T. and Franklin, Bernardo S. and Nickenig,
                    Georg and Strassburg, Christian P. and Plat, Jogchum and
                    Sauerbruch, Tilman and Latz, Eicke and Lütjohann, Dieter
                    and Zimmer, Sebastian and Trebicka, Jonel},
  Title           = {Statins improve {NASH} via inhibition of {RhoA} and
                    Ras},
  JournalTitle    = {Am. J. Physiol.-Gastroint. Liver Physiol.},
  Date            = {2016},
  DOI             = {10.1152/ajpgi.00063.2016},
  Keywords        = {Animals,apoE,Apolipoproteins
                    E,Cholesterol,Diet,Western,GTPase,Hydroxymethylglutaryl-CoA
                    Reductase Inhibitors,Liver,liver
                    fibrosis,Mice,Mice,Knockout,NASH,Non-alcoholic Fatty
                    Liver Disease,ras Proteins,rhoA GTP-Binding
                    Protein,Signal Transduction,Simvastatin,statins,Western
                    diet},
  Number          = {4},
  Pages           = {G724--G733},
  Volume          = {311}
}

@Article{schnabl2014a,
  Author          = {Schnabl, Bernd and Brenner, David A.},
  Title           = {Interactions Between the Intestinal Microbiome and Liver
                    Diseases},
  JournalTitle    = {Gastroenterology},
  Date            = {2014},
  DOI             = {10.1053/j.gastro.2014.01.020},
  Number          = {6},
  Pages           = {1513--1524},
  Volume          = {146}
}

@Article{schneider2015a,
  Author          = {Schneider, Kai Markus and Bieghs, Veerle and Heymann,
                    Felix and Hu, Wei and Dreymueller, Daniela and Liao,
                    Lijun and Frissen, Mick and Ludwig, Andreas and Gassler,
                    Nikolaus and Pabst, Oliver and Latz, Eicke and Sellge,
                    Gernot and Penders, John and Tacke, Frank and Trautwein,
                    Christian},
  Title           = {{CX3CR1} is a gatekeeper for intestinal barrier
                    integrity in mice: {Limiting} steatohepatitis by
                    maintaining intestinal homeostasis},
  JournalTitle    = {Hepatology},
  Date            = {2015},
  Addendum        = equal,
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1002/hep.27982},
  ids             = {Schneider:729715},
  Keywords        = {SchneiderKM-Selection},
  Note            = {*equal contribution},
  Number          = {5},
  Pages           = {1405--1416},
  Volume          = {62}
}

@Article{schneider2016b,
  Author          = {Schneider, Kai Markus and Bieghs, Veerle and Pabst,
                    Oliver and Trautwein, Christian},
  Title           = {Reply},
  JournalTitle    = {Hepatology},
  Date            = {2015},
  DOI             = {10.1002/hep.28145},
  Number          = {1},
  Pages           = {304--305},
  Subtitle        = {CORRESPONDENCE},
  Volume          = {64}
}

@Article{schneider2018a,
  Author          = {Schneider, Kai Markus and Albers, Stefanie and
                    Trautwein, Christian},
  Title           = {Role of bile acids in the gut-liver axis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2018},
  DOI             = {10.1016/j.jhep.2017.11.025},
  Keywords        = {SchneiderKM-Selection},
  Number          = {5},
  Pages           = {1083--1085},
  Volume          = {68}
}

@Article{schneider2020b,
  Author          = {Schneider, Carolin V. and Hamesch, Karim and Gross,
                    Annika and Mandorfer, Mattias and Moeller, Linda S. and
                    Pereira, Vitor and Pons, Monica and Kuca, Pawel and
                    Reichert, Matthias C. and Benini, Federica and Burbaum,
                    Barbara and Voss, Jessica and Gutberlet, Marla and
                    Woditsch, Vivien and Lindhauer, Cecilia and Fromme, Malin
                    and Kümpers, Julia and Bewersdorf, Lisa and Schaefer,
                    Benedikt and Eslam, Mohammed and Bals, Robert and
                    Janciauskiene, Sabina and Carvão, Joana and Neureiter,
                    Daniel and Zhou, Biaohuan and Wöran, Katharina and
                    Bantel, Heike and Geier, Andreas and Dirrichs, Timm and
                    Stickel, Felix and Teumer, Alexander and Verbeek, Jef and
                    Nevens, Frederik and Govaere, Olivier and Krawczyk,
                    Marcin and Roskams, Tania and Haybaeck, Johannes and
                    Lurje, Georg and Chorostowska-Wynimko, Joanna and
                    Genesca, Joan and Reiberger, Thomas and Lammert, Frank
                    and Krag, Aleksander and George, Jacob and Anstee,
                    Quentin M. and Trauner, Michael and Datz, Christian and
                    Gaisa, Nadine T. and Denk, Helmut and Trautwein,
                    Christian and Aigner, Elmar and Strnad, Pavel},
  Title           = {Liver Phenotypes of {European} Adults Heterozygous or
                    Homozygous for {Pi*Z} Variant of {AAT} {(Pi*MZ} vs
                    {Pi*ZZ} genotype) and Noncarriers},
  JournalTitle    = {Gastroenterology},
  Addendum        = equalpreliminarywork,
  Date            = {2020},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1053/j.gastro.2020.04.058},
  Keywords        = {SchneiderCV-Selection,Strnad-Selection},
  Note            = {*equal contribution},
  Number          = {2},
  Pages           = {534--548.e11},
  Volume          = {159}
}

@Article{schneider2021b,
  Author          = {Schneider, Carolin V. and Schneider, Kai Markus and
                    Conlon, Donna M. and Park, Joseph and Vujkovic, Marijana
                    and Zandvakili, Inuk and Ko, Yi-An and Trautwein,
                    Christian and Carr, Rotonya M. and Strnad, Pavel and
                    Thaiss, Christoph A. and Rader, Daniel J.},
  Title           = {A genome-first approach to mortality and metabolic
                    phenotypes in {MTARC1} {p.Ala165Thr} (rs2642438)
                    heterozygotes and homozygotes},
  JournalTitle    = {Med},
  Date            = {2021},
  author+an:default = {1=equal;2=equal},
  Addendum        = equal,
  DOI             = {10.1016/j.medj.2021.04.011},
  Keywords        = {SchneiderCV-Selection,SchneiderKM-Selection},
  Number          = {7},
  Pages           = {851--863.e3},
  Volume          = {2}
}

@Article{schneider2021c,
  Author          = {Schneider, Carolin V. and Fromme, Malin and Schneider,
                    Kai Markus and Bruns, Tony and Strnad, Pavel},
  Title           = {Mortality in Patients With Genetic and Environmental
                    Risk of Liver Disease},
  JournalTitle    = {Am. J. Gastroenterol.},
  Date            = {2021},
  DOI             = {10.14309/ajg.0000000000001326},
  Keywords        = {SchneiderCV-Selection},
  Number          = {8},
  Pages           = {1741--1745},
  Volume          = {116}
}

@Article{schneider2021d,
  Author          = {Schneider, Carolin V. and Zandvakili, Inuk and Thaiss,
                    Christoph A. and Schneider, Kai Markus},
  Title           = {Physical activity is associated with reduced risk of
                    liver disease in the prospective {UK} Biobank cohort},
  JournalTitle    = {JHEP Reports},
  Date            = {2021},
  Addendum        = preliminarywork,
  DOI             = {10.1016/j.jhepr.2021.100263},
  Keywords        = {SchneiderCV-Selection,SchneiderKM-Selection},
  Number          = {3},
  Pages           = {100263},
  Volume          = {3}
}

@Article{schneider2021e,
  Author          = {Schneider, Carolin V. and Strnad, Pavel},
  Title           = {{SARS}-{CoV}-2 infection in alpha1-antitrypsin
                    deficiency},
  JournalTitle    = {Resp. Med.},
  Date            = {2021},
  DOI             = {10.1016/j.rmed.2021.106466},
  Keywords        = {SchneiderCV-Selection},
  Number          = {106466},
  Pages           = {106466},
  Volume          = {184}
}

@Article{schneider2022a,
  Author          = {Schneider, Kai Markus and Mohs, Antje and Gui, Wenfang
                    and Galvez, Eric J. C. and Candels, Lena Susanna and
                    Hoenicke, Lisa and Muthukumarasamy, Uthayakumar and
                    Holland, Christian H. and Elfers, Carsten and Kilic,
                    Konrad and Schneider, Carolin Victoria and Schierwagen,
                    Robert and Strnad, Pavel and Wirtz, Theresa H. and
                    Marschall, Hanns-Ulrich and Latz, Eicke and Lelouvier,
                    Benjamin and Saez-Rodriguez, Julio and de Vos, Willem and
                    Strowig, Till and Trebicka, Jonel and Trautwein,
                    Christian},
  Title           = {Imbalanced gut microbiota fuels hepatocellular carcinoma
                    development by shaping the hepatic inflammatory
                    microenvironment},
  JournalTitle    = {Nat. Commun.},
  Addendum        = equal,
  Date            = {2022},
  author+an:default = {1=equal;2=equal},
  DOI             = {10.1038/s41467-022-31312-5},
  Keywords        = {Mohs-Selection,SchneiderKM-Selection,Trautwein-Selection,Wirtz-Selection},
  Number          = {1},
  Pages           = {3964},
  Volume          = {13}
}

@Article{schoenfeld2016a,
  Author          = {Schreuder, Tim C. M. A. and Marsman, Hendrik A. and
                    Lenicek, Martin and van Werven, Jochem R. and Nederveen,
                    Aart J. and Jansen, Peter L. M. and Schaap, Frank G.},
  Title           = {Advances in {IBS} 2016: {A} Review of Current and
                    Emerging Data},
  JournalTitle    = {Gastroenterol. Hepatol.},
  Date            = {2016},
  Pages           = {1--11},
  Volume          = {12}
}

@Article{Scott2018-iw,
  Author          = {Scott, Nicholas A. and Andrusaite, Anna and Andersen,
                    Peter and Lawson, Melissa and Alcon-Giner, Cristina and
                    Leclaire, Charlotte and Caim, Shabhonam and Le Gall,
                    Gwenaelle and Shaw, Tovah and Connolly, James P. R. and
                    Roe, Andrew J. and Wessel, Hannah and Bravo-Blas, Alberto
                    and Thomson, Carolyn A. and Kästele, Verena and Wang,
                    Ping and Peterson, Daniel A. and Bancroft, Allison and
                    Li, Xuhang and Grencis, Richard and Mowat, Allan McI and
                    Hall, Lindsay J. and Travis, Mark A. and Milling, Simon
                    W. F. and Mann, Elizabeth R.},
  Title           = {Antibiotics induce sustained dysregulation of intestinal
                    T cell immunity by perturbing macrophage homeostasis},
  JournalTitle    = {Sci. Transl. Med.},
  Date            = {2018},
  DOI             = {10.1126/scitranslmed.aao4755},
  Number          = {464},
  Volume          = {10}
}

@Article{Morita2019-ke,
  Author          = {Morita, Naoki and Umemoto, Eiji and Fujita, Setsuko and
                    Hayashi, Akio and Kikuta, Junichi and Kimura, Ikuo and
                    Haneda, Takeshi and Imai, Toshio and Inoue, Asuka and
                    Mimuro, Hitomi and Maeda, Yuichi and Kayama, Hisako and
                    Okumura, Ryu and Aoki, Junken and Okada, Nobuhiko and
                    Kida, Toshiyuki and Ishii, Masaru and Nabeshima, Ryusuke
                    and Takeda, Kiyoshi},
  Title           = {{GPR31}-dependent dendrite protrusion of intestinal
                    {CX3CR1+} cells by bacterial metabolites},
  JournalTitle    = {Nature},
  Date            = {2019},
  DOI             = {10.1038/s41586-019-0884-1},
  Number          = {7742},
  Pages           = {110--114},
  Volume          = {566}
}

@Article{scorletti2022a,
  Author          = {Scorletti, Eleonora and Creasy, Kate Townsend and
                    Vujkovic, Marijana and Vell, Mara and Zandvakili, Inuk
                    and Rader, Daniel J. and Schneider, Kai Markus and
                    Schneider, Carolin V.},
  Title           = {Dietary Vitamin E Intake Is Associated With a Reduced
                    Risk of Developing Digestive Diseases and Nonalcoholic
                    Fatty Liver Disease},
  JournalTitle    = {Am. J. Gastroenterol.},
  Date            = {2022},
  DOI             = {10.14309/ajg.0000000000001726},
  Keywords        = {SchneiderCV-Selection},
  Number          = {6},
  Pages           = {927--930},
  Volume          = {117}
}

@Article{sender2016a,
  Author          = {Sender, Ron and Fuchs, Shai and Milo, Ron},
  Title           = {Revised Estimates for the Number of Human and Bacteria
                    Cells in the Body},
  JournalTitle    = {PLOS Biol.},
  Date            = {2016},
  DOI             = {10.1371/journal.pbio.1002533},
  Number          = {8},
  Pages           = {e1002533},
  Volume          = {14}
}

@Article{Sorribas2019-ur,
  Author          = {Sorribas, Marcel and Jakob, Manuel O and Yilmaz,
                    Bahtiyar and Li, Hai and Stutz, David and Noser, Yannik
                    and de Gottardi, Andrea and Moghadamrad, Sheida and
                    Hassan, Moshin and Albillos, Agustin and Francés, Ruben
                    and Juanola, Oriol and Spadoni, Ilaria and Rescigno,
                    Maria and Wiest, Reiner},
  Title           = {{FXR} modulates the gut-vascular barrier by regulating
                    the entry sites for bacterial translocation in
                    experimental cirrhosis},
  JournalTitle    = {J. Hepatol.},
  Date            = {2019},
  DOI             = {10.1016/j.jhep.2019.06.017},
  Number          = {6},
  Pages           = {1126--1140},
  Volume          = {71}
}

@Article{Maccioni2020-lz,
  Author          = {Maccioni, Luca and Gao, Bei and Leclercq, Sophie and
                    Pirlot, Boris and Horsmans, Yves and De Timary, Philippe
                    and Leclercq, Isabelle and Fouts, Derrick and Schnabl,
                    Bernd and Stärkel, Peter},
  Title           = {Intestinal permeability, microbial translocation,
                    changes in duodenal and fecal microbiota, and their
                    associations with alcoholic liver disease progression in
                    humans},
  JournalTitle    = {Gut Microbes},
  Date            = {2020},
  DOI             = {10.1080/19490976.2020.1782157},
  Number          = {1},
  Pages           = {1782157},
  Volume          = {12}
}

@Article{Seo2020-yz,
  Author          = {Seo, Boram and Jeon, Kyungchan and Moon, Sunghyun and
                    Lee, Kiuk and Kim, Woon-Ki and Jeong, Hyein and Cha,
                    Kwang Hyun and Lim, Mi Young and Kang, Wondae and Kweon,
                    Mi-Na and Sung, Joohon and Kim, Won and Park, Joo-Hong
                    and Ko, GwangPyo},
  Title           = {Roseburia spp. Abundance Associates with Alcohol
                    Consumption in Humans and Its Administration Ameliorates
                    Alcoholic Fatty Liver in Mice},
  JournalTitle    = {Cell Host Microbe},
  Date            = {2020},
  DOI             = {10.1016/j.chom.2019.11.001},
  Number          = {1},
  Pages           = {25--40.e6},
  Volume          = {27}
}

@Article{seo2019a,
  Author          = {Seo, Wonhyo and Gao, Yanhang and He, Yong and Sun, Jing
                    and Xu, Hongqin and Feng, Dechun and Park, Seol Hee and
                    Cho, Young-Eun and Guillot, Adrien and Ren, Tianyi and
                    Wu, Ruihong and Wang, Jingyun and Kim, Seung-Jin and
                    Hwang, Seonghwan and Liangpunsakul, Suthat and Yang,
                    Yingzi and Niu, Junqi and Gao, Bin},
  Title           = {{ALDH2} deficiency promotes alcohol-associated liver
                    cancer by activating oncogenic pathways via oxidized
                    {DNA}-enriched extracellular vesicles},
  JournalTitle    = {J. Hepatol.},
  Date            = {2019},
  DOI             = {10.1016/j.jhep.2019.06.018},
  Issue           = {71},
  Keywords        = {Guillot-Selection},
  Number          = {5},
  Pages           = {1000--1011},
  Volume          = {71}
}

@Article{sethi2017a,
  Author          = {Sethi, Maya K. and Thol, Felicitas and Stadler, Michael
                    and Heuser, Michael and Ganser, Arnold and Koenecke,
                    Christian and Pabst, Oliver},
  Title           = {{VH1} Family Immunoglobulin Repertoire Sequencing after
                    Allogeneic Hematopoietic Stem Cell Transplantation},
  JournalTitle    = {PLoS One},
  Date            = {2017},
  DOI             = {10.1371/journal.pone.0168096},
  ids             = {Sethi:685336},
  Keywords        = {Peer-B06},
  Number          = {1},
  Pages           = {e0168096},
  Volume          = {12}
}

@Article{shetty2018a,
  Author          = {Shetty, Shishir and Lalor, Patricia F. and Adams, David
                    H.},
  Title           = {Liver sinusoidal endothelial cells — gatekeepers of
                    hepatic immunity},
  JournalTitle    = {Nat. Rev. Gastroenterol. Hepatol.},
  Date            = {2018},
  DOI             = {10.1038/s41575-018-0020-y},
  Number          = {9},
  Pages           = {555--567},
  Volume          = {15}
}

@Article{shulzhenko2011a,
  Author          = {Shulzhenko, Natalia and Morgun, Andrey and Hsiao,
                    William and Battle, Michele and Yao, Michael and
                    Gavrilova, Oksana and Orandle, Marlene and Mayer, Lloyd
                    and Macpherson, Andrew J and McCoy, Kathy D and
                    Fraser-Liggett, Claire and Matzinger, Polly},
  Title           = {Crosstalk between B lymphocytes, microbiota and the
                    intestinal epithelium governs immunity versus metabolism
                    in the gut},
  JournalTitle    = {Nat. Med.},
  Date            = {2011},
  DOI             = {10.1038/nm.2505},
  Number          = {12},
  Pages           = {1585--1593},
  Volume          = {17}
}

@Article{Bertocchi2021,
  Author          = {Bertocchi, Alice and Carloni, Sara and Ravenda, Paola
                    Simona and Bertalot, Giovanni and Spadoni, Ilaria and
                    Cascio, Antonino Lo and Gandini, Sara and Lizier, Michela
                    and Braga, Daniele and Asnicar, Francesco and Segata,
                    Nicola and Klaver, Chris and Brescia, Paola and Rossi,
                    Elio and Anselmo, Achille and Guglietta, Silvia and
                    Maroli, Annalisa and Spaggiari, Paola and Tarazona,
                    Noelia and Cervantes, Andres and Marsoni, Silvia and
                    Lazzari, Luca and Jodice, Maria Giovanna and Luise,
                    Chiara and Erreni, Marco and Pece, Salvatore and Fiore,
                    Pier Paolo Di and Viale, Giuseppe and Spinelli, Antonino
                    and Pozzi, Chiara and Penna, Giuseppe and Rescigno,
                    Maria},
  Title           = {Gut vascular barrier impairment leads to intestinal
                    bacteria dissemination and colorectal cancer metastasis
                    to liver},
  JournalTitle    = {Cancer Cell},
  Date            = {2021},
  DOI             = {10.1016/j.ccell.2021.03.004},
  Number          = {5},
  Pages           = {708--724.e11},
  Volume          = {39}
}

@Article{spadoni2015a,
  Author          = {Spadoni, Ilaria and Zagato, Elena and Bertocchi, Alice
                    and Paolinelli, Roberta and Hot, Edina and Di Sabatino,
                    Antonio and Caprioli, Flavio and Bottiglieri, Luca and
                    Oldani, Amanda and Viale, Giuseppe and Penna, Giuseppe
                    and Dejana, Elisabetta and Rescigno, Maria},
  Title           = {A gut-vascular barrier controls the systemic
                    dissemination of bacteria},
  JournalTitle    = {Science},
  Date            = {2015},
  DOI             = {10.1126/science.aad0135},
  Number          = {6262},
  Pages           = {830--834},
  Volume          = {350}
}

@Article{spadoni2017a,
  Author          = {Spadoni, Ilaria and Fornasa, Giulia and Rescigno,
                    Maria},
  Title           = {Organ-specific protection mediated by cooperation
                    between vascular and epithelial barriers},
  JournalTitle    = {Nat. Rev. Immunol.},
  Date            = {2017},
  DOI             = {10.1038/nri.2017.100},
  Number          = {12},
  Pages           = {761--773},
  Volume          = {17}
}

@Article{suski2022a,
  Author          = {Suski, Jan M. and Ratnayeke, Nalin and Braun, Marcin and
                    Zhang, Tian and Strmiska, Vladislav and Michowski,
                    Wojciech and Can, Geylani and Simoneau, Antoine and
                    Snioch, Konrad and Cup, Mikolaj and Sullivan, Caitlin M.
                    and Wu, Xiaoji and Nowacka, Joanna and Branigan, Timothy
                    B. and Pack, Lindsey R. and DeCaprio, James A. and Geng,
                    Yan and Zou, Lee and Gygi, Steven P. and Walter, Johannes
                    C. and Meyer, Tobias and Sicinski, Piotr},
  Title           = {{CDC7}-independent {G1/S} transition revealed by
                    targeted protein degradation},
  JournalTitle    = {Nature},
  Date            = {2022},
  DOI             = {10.1038/s41586-022-04698-x},
  Number          = {7909},
  Pages           = {357--365},
  Volume          = {605}
}

@Article{Thibaut2022-bs,
  Author          = {Thibaut, Morgane M. and Bindels, Laure B.},
  Title           = {Crosstalk between bile acid-activated receptors and
                    microbiome in entero-hepatic inflammation},
  JournalTitle    = {Trends Mol. Med.},
  Date            = {2022},
  DOI             = {10.1016/j.molmed.2021.12.006},
  Keywords        = {bile acids; cholestatic disease; gut microbiota;
                    inflammatory bowel disease; intestinal inflammation;
                    microbial metabolism},
  Number          = {3},
  Pages           = {223--236},
  Volume          = {28}
}

@Article{thiel2015a,
  Author          = {Thiel, Christoph and Schneckener, Sebastian and Krauss,
                    Markus and Ghallab, Ahmed and Hofmann, Ute and Kanacher,
                    Tobias and Zellmer, Sebastian and Gebhardt, Rolf and
                    Hengstler, Jan G. and Kuepfer, Lars},
  Title           = {A Systematic Evaluation of the Use of Physiologically
                    Based Pharmacokinetic Modeling for Cross-Species
                    Extrapolation},
  JournalTitle    = {J. Pharm. Sci-us.},
  Date            = {2015},
  DOI             = {10.1002/jps.24214},
  Keywords        = {Küpfer-Selection},
  Number          = {1},
  Pages           = {191--206},
  Volume          = {104}
}

@Article{thiel2018a,
  Author          = {Thiel, Christoph and Smit, Ines and Baier, Vanessa and
                    Cordes, Henrik and Fabry, Brigida and Blank, Lars Mathias
                    and Kuepfer, Lars},
  Title           = {Using quantitative systems pharmacology to evaluate the
                    drug efficacy of {COX}-2 and 5-{LOX} inhibitors in
                    therapeutic situations},
  JournalTitle    = {npj Syst. Biol. Appl.},
  Date            = {2018},
  DOI             = {10.1038/s41540-018-0062-3},
  Keywords        = {Küpfer-Selection},
  Number          = {1},
  Volume          = {4}
}

@Article{Roderburg2019-bn,
  Author          = {Roderburg, Christoph and Berres, Marie-Luise and Wree,
                    Alexander and Loosen, Sven H and Luedde, Tom and
                    Trautwein, Christian},
  Title           = {Excellent response to {anti-PD-1} therapy in a patient
                    with hepatocellular carcinoma intolerant to sorafenib},
  JournalTitle    = {Visc. Med.},
  Date            = {2019},
  DOI             = {10.1159/000497465},
  Keywords        = {Hepatocellular carcinoma; Nivolumab; PD-L1; Response},
  Number          = {1},
  Pages           = {43--46},
  Addendum        = preliminarywork,
  Volume          = {35}
}

@Article{thuering2019a,
  Author          = {Thüring, J. and Zimmermann, M. and Bruners, P. and
                    Pedersoli, F. and Schulze-Hagen, M. and Barzakova, E. and
                    Kuhl, C. K. and Isfort, P.},
  Title           = {Short-Term Oral Sorafenib for Therapy of Intratumoral
                    Shunts of Hepatocellular Carcinoma to Enable
                    Intraarterial Treatment},
  JournalTitle    = {CardioVasc. Interv. Radiol.},
  Date            = {2019},
  DOI             = {10.1007/s00270-019-02294-7},
  Keywords        = {Barzakova-Selection},
  Number          = {10},
  Pages           = {1494--1499},
  Volume          = {42}
}

@Article{tilg2016a,
  Author          = {Tilg, Herbert and Cani, Patrice D and Mayer, Emeran A},
  Title           = {Gut microbiome and liver diseases},
  JournalTitle    = {Gut},
  Date            = {2016},
  DOI             = {10.1136/gutjnl-2016-312729},
  Number          = {12},
  Pages           = {2035--2044},
  Volume          = {65}
}

@Article{tripathi_simvastatin_2018,
  Author          = {Tripathi, Dinesh Mani and Vilaseca, Marina and Lafoz,
                    Erica and Garcia-Calderó, Héctor and Viegas Haute,
                    Gabriela and Fernández-Iglesias, Anabel and Rodrigues de
                    Oliveira, Jarbas and García-Pagán, Juan Carlos and
                    Bosch, Jaime and Gracia-Sancho, Jordi},
  Title           = {Simvastatin Prevents Progression of Acute on Chronic
                    Liver Failure in Rats With Cirrhosis and Portal
                    Hypertension},
  JournalTitle    = {Gastroenterology},
  Date            = {2018},
  DOI             = {10.1053/j.gastro.2018.07.022},
  Number          = {5},
  Pages           = {1564--1577},
  Volume          = {155}
}

@Article{turchaninova2016a,
  Author          = {Turchaninova, M A and Davydov, A and Britanova, O V and
                    Shugay, M and Bikos, V and Egorov, E S and Kirgizova, V I
                    and Merzlyak, E M and Staroverov, D B and Bolotin, D A
                    and Mamedov, I Z and Izraelson, M and Logacheva, M D and
                    Kladova, O and Plevova, K and Pospisilova, S and
                    Chudakov, D M},
  Title           = {High-quality full-length immunoglobulin profiling with
                    unique molecular barcoding},
  JournalTitle    = {Nat. Protoc.},
  Date            = {2016},
  DOI             = {10.1038/nprot.2016.093},
  Number          = {9},
  Pages           = {1599--1616},
  Volume          = {11}
}

@Article{turqueti-neves2015a,
  Author          = {Turqueti-Neves, Adriana and Otte, Manuel and Schwartz,
                    Christian and Schmitt, Michaela Erika Renate and Lindner,
                    Cornelia and Pabst, Oliver and Yu, Philipp and
                    Voehringer, David},
  Title           = {The Extracellular Domains of {IgG1} and T Cell-Derived
                    {IL}-{4/IL}-13 Are Critical for the Polyclonal Memory
                    {IgE} Response In Vivo},
  JournalTitle    = {PLOS Biol.},
  Date            = {2015},
  DOI             = {10.1371/journal.pbio.1002290},
  Keywords        = {Peer-B06},
  Note            = {and T Cell-Derived IL-4/IL-13 Are Critical for the
                    Polyclonal Memory IgE Response In Vivo. PLoS biology
                    13:e1002290.},
  Number          = {11},
  Pages           = {e1002290},
  Volume          = {13}
}

@Article{ubeda2012a,
  Author          = {Ubeda, Carles and Lipuma, Lauren and Gobourne, Asia and
                    Viale, Agnes and Leiner, Ingrid and Equinda, Michele and
                    Khanin, Raya and Pamer, Eric G.},
  Title           = {Familial transmission rather than defective innate
                    immunity shapes the distinct intestinal microbiota of
                    {TLR}-deficient mice},
  JournalTitle    = {J. Exp. Med.},
  Date            = {2012},
  DOI             = {10.1084/jem.20120504},
  Number          = {8},
  Pages           = {1445--1456},
  Volume          = {209}
}

@Article{CespedesFeliciano2017,
  Author          = {Feliciano, Elizabeth M. Cespedes and Kroenke, Candyce H.
                    and Meyerhardt, Jeffrey A. and Prado, Carla M. and
                    Bradshaw, Patrick T. and Kwan, Marilyn L. and Xiao,
                    Jingjie and Alexeeff, Stacey and Corley, Douglas and
                    Weltzien, Erin and Castillo, Adrienne L. and Caan, Bette
                    J.},
  Title           = {Association of Systemic Inflammation and Sarcopenia With
                    Survival in Nonmetastatic Colorectal Cancer},
  JournalTitle    = {JAMA Oncology},
  Date            = {2017},
  DOI             = {10.1001/jamaoncol.2017.2319},
  Number          = {12},
  Pages           = {e172319},
  Volume          = {3}
}

@Article{Hegde2021,
  Author          = {Hegde, Samarth and Leader, Andrew M. and Merad, Miriam},
  Title           = {{MDSC}: Markers, development, states, and unaddressed
                    complexity},
  JournalTitle    = {Immunity},
  Date            = {2021},
  DOI             = {10.1016/j.immuni.2021.04.004},
  Number          = {5},
  Pages           = {875--884},
  Volume          = {54}
}

@Article{Fearon2011,
  Author          = {Fearon, Kenneth and Strasser, Florian and Anker, Stefan
                    D and Bosaeus, Ingvar and Bruera, Eduardo and Fainsinger,
                    Robin L and Jatoi, Aminah and Loprinzi, Charles and
                    MacDonald, Neil and Mantovani, Giovanni and Davis, Mellar
                    and Muscaritoli, Maurizio and Ottery, Faith and Radbruch,
                    Lukas and Ravasco, Paula and Walsh, Declan and Wilcock,
                    Andrew and Kaasa, Stein and Baracos, Vickie E},
  Title           = {Definition and classification of cancer cachexia: an
                    international consensus},
  JournalTitle    = {The Lancet Oncology},
  Date            = {2011},
  DOI             = {10.1016/s1470-2045(10)70218-7},
  Number          = {5},
  Pages           = {489--495},
  Volume          = {12}
}

@Article{Biswas2020,
  Author          = {Biswas, Anup K. and Acharyya, Swarnali},
  Title           = {Understanding cachexia in the context of metastatic
                    progression},
  JournalTitle    = {Nat. Rev. Cancer},
  Date            = {2020},
  DOI             = {10.1038/s41568-020-0251-4},
  Number          = {5},
  Pages           = {274--284},
  Volume          = {20}
}

@Article{vanBest:793496,
  Author          = {van Best, Niels and Rolle-Kampczyk, U. and Schaap, Frank
                    G. and Basic, M. and Olde Damink, Steven W. M. and
                    Bleich, A. and Savelkoul, P. and von Bergen, Martin and
                    Penders, J. and Hornef, Mathias W.},
  Title           = {Bile acids drive the newborn’s gut microbiota
                    maturation},
  JournalTitle    = {Nat. Commun.},
  Date            = {2020},
  DOI             = {10.1038/s41467-020-17183-8},
  Keywords        = {von
                    Bergen-Selection,Schaap-Selection,Hornef-Selection,CRC1382-Project
                    B01,CRC1382-Project Q03,CRC1382-Project
                    A07,CRC1382-Project A07,CRC1382-Project A05},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Pages           = {3692},
  Volume          = {11}
}

@Article{vanBest:812236,
  Author          = {van Best, Niels and Trepels-Kottek, Sonja and Savelkoul,
                    Paul and Orlikowsky, Thorsten and Hornef, Mathias W. and
                    Penders, John},
  Title           = {Influence of probiotic supplementation on the developing
                    microbiota in human preterm neonates},
  JournalTitle    = {Gut microbes},
  Date            = {2020},
  author+an:default = {4=equal;5=equal;6=equal},
  Addendum        = equal,
  DOI             = {10.1080/19490976.2020.1826747},
  Keywords        = {,CRC1382-Project B01,CRC1382-Project Q03},
  Note            = {SFB 1382: Die Darm-Leber-Achse -- Funktionelle
                    Zusammenhänge und therapeutische Strategien
                    (403224013)},
  Number          = {1},
  Pages           = {1826747},
  Volume          = {12}
}

@Article{vanMierlo:687670,
  Author          = {van Mierlo, Kim M.C. and Schaap, Frank G. and Dejong,
                    Cornelis H.C. and Olde Damink, Steven W. M.},
  Title           = {Liver resection for cancer: {New} developments in
                    prediction, prevention and management of postresectional
                    liver failure},
  JournalTitle    = {J. Hepatol.},
  Date            = {2016},
  DOI             = {10.1016/j.jhep.2016.06.006},
  Keywords        = {Olde Damink-Selection},
  Number          = {6},
  Pages           = {1217--1231},
  Volume          = {65}
}

@Article{vanSchaik2012,
  Author          = {van Schaik, Fiona D. M. and Gadaleta, Raffaella M. and
                    Schaap, Frank G. and van Mil, Saskia W. C. and Siersema,
                    Peter D. and Oldenburg, Bas and van Erpecum, Karel J.},
  Title           = {Pharmacological Activation of the Bile Acid Nuclear
                    Farnesoid X Receptor Is Feasible in Patients with
                    Quiescent Crohn's Colitis},
  JournalTitle    = {PLoS ONE},
  Date            = {2012},
  DOI             = {10.1371/journal.pone.0049706},
  Editor          = {Makishima, Makoto},
  Number          = {11},
  Pages           = {e49706},
  Volume          = {7}
}

@Article{vandenBroek2011,
  Author          = {van den Broek, Maartje A.J. and Bloemen, Johanne G. and
                    Dello, Simon A.W.G. and van de Poll, Marcel C.G. and Olde
                    Damink, Steven W.M. and Dejong, Cornelis H.C.},
  Title           = {Randomized controlled trial analyzing the effect of 15
                    or 30 min intermittent Pringle maneuver on hepatocellular
                    damage during liver surgery},
  JournalTitle    = {J. Hepatol.},
  Date            = {2011},
  DOI             = {10.1016/j.jhep.2010.11.024},
  Keywords        = {Olde Damink-Selection},
  Number          = {2},
  Pages           = {337--345},
  Volume          = {55}
}

@Article{vehreschild2022a,
  Author          = {Vehreschild, Maria J. G. T. and Ducher, Annie and Louie,
                    Thomas and Cornely, Oliver A. and Feger, Celine and Dane,
                    Aaron and Varastet, Marina and Vitry, Fabien and de
                    Gunzburg, Jean and Andremont, Antoine and Mentré, France
                    and Wilcox, Mark H.},
  Title           = {An open randomized multicentre Phase 2 trial to assess
                    the safety of {DAV132} and its efficacy to protect gut
                    microbiota diversity in hospitalized patients treated
                    with fluoroquinolones},
  JournalTitle    = {J. Antimicrob. Chemoth.},
  Date            = {2022},
  DOI             = {10.1093/jac/dkab474},
  Keywords        = {Vehreschild-Selection},
  Number          = {4},
  Pages           = {1155--1165},
  Volume          = {77}
}

@Article{Blackburn2022-dg,
  Author          = {Blackburn, Jessica B. and Schaff, Jacob A. and Gutor,
                    Sergey and Du, Rui-Hong and Nichols, David and Sherrill,
                    Taylor and Gutierrez, Austin J. and Xin, Matthew K. and
                    Wickersham, Nancy and Zhang, Yong and Holtzman, Michael
                    J. and Ware, Lorraine B. and Banovich, Nicholas E. and
                    Kropski, Jonathan A. and Blackwell, Timothy S. and
                    Richmond, Bradley W.},
  Title           = {Secretory Cells Are the Primary Source of {pIgR} in
                    Small Airways},
  JournalTitle    = {Am. J. Resp. Cell Mol.},
  Date            = {2022},
  DOI             = {10.1165/rcmb.2021-0548oc},
  Number          = {3},
  Pages           = {334--345},
  Volume          = {67}
}

@Article{Penny2022-bv,
  Author          = {Penny, Hugo A. and Domingues, Rita G. and Krauss, Maria
                    Z. and Melo-Gonzalez, Felipe and Lawson, Melissa A. E.
                    and Dickson, Suzanna and Parkinson, James and Hurry,
                    Madeleine and Purse, Catherine and Jegham, Emna and
                    Godinho-Silva, Cristina and Rendas, Miguel and
                    Veiga-Fernandes, Henrique and Bechtold, David A. and
                    Grencis, Richard K. and Toellner, Kai-Michael and
                    Waisman, Ari and Swann, Jonathan R. and Gibbs, Julie E.
                    and Hepworth, Matthew R.},
  Title           = {Rhythmicity of intestinal {IgA} responses confers
                    oscillatory commensal microbiota mutualism},
  JournalTitle    = {Sci. Immunol.},
  Date            = {2022},
  DOI             = {10.1126/sciimmunol.abk2541},
  Number          = {75},
  Volume          = {7}
}

@Article{velaga2009a,
  Author          = {Velaga, Sarvari and Herbrand, Heike and Friedrichsen,
                    Michaela and Jiong, Tian and Dorsch, Martina and
                    Hoffmann, Matthias W. and Förster, Reinhold and Pabst,
                    Oliver},
  Title           = {Chemokine Receptor {CXCR5} Supports Solitary Intestinal
                    Lymphoid Tissue Formation, B Cell Homing, and Induction
                    of Intestinal {IgA} Responses},
  JournalTitle    = {J. Immunol.},
  Date            = {2009},
  DOI             = {10.4049/jimmunol.0801141},
  Number          = {5},
  Pages           = {2610--2619},
  Volume          = {182}
}

@Article{vidal-lletjos2019a,
  Author          = {Vidal-Lletjós, Sandra and Andriamihaja, Mireille and
                    Blais, Anne and Grauso, Marta and Lepage, Patricia and
                    Davila, Anne-Marie and Gaudichon, Claire and Leclerc,
                    Marion and Blachier, François and Lan, Annaïg},
  Title           = {Mucosal healing progression after acute colitis in
                    mice},
  JournalTitle    = {World J. Gastroenterol.},
  Date            = {2019},
  DOI             = {10.3748/wjg.v25.i27.3572},
  Number          = {27},
  Pages           = {3572--3589},
  Volume          = {25}
}

@Article{Van_Meer2016-ul,
  Author          = {van Meer, Suzanne and van Erpecum, Karel J. and
                    Sprengers, Dave and Coenraad, Minneke J. and Klümpen,
                    Heinz-Josef and Jansen, Peter L.M. and IJzermans, Jan
                    N.M. and Verheij, Joanne and van Nieuwkerk, Carin M.J.
                    and Siersema, Peter D. and de Man, Robert A.},
  Title           = {Hepatocellular carcinoma in cirrhotic versus
                    noncirrhotic livers},
  JournalTitle    = {Eur. J. Gastroenterol. Hepatol.},
  Date            = {2016},
  DOI             = {10.1097/meg.0000000000000527},
  Number          = {3},
  Pages           = {352--359},
  Subtitle        = {results from a large cohort in the Netherlands},
  Volume          = {28}
}

@Article{voedisch2009a,
  Author          = {Voedisch, Sabrina and Koenecke, Christian and David,
                    Sascha and Herbrand, Heike and Förster, Reinhold and
                    Rhen, Mikael and Pabst, Oliver},
  Title           = {Mesenteric Lymph Nodes Confine Dendritic Cell-Mediated
                    Dissemination of \emph{Salmonella enterica} Serovar
                    Typhimurium and Limit Systemic Disease in Mice},
  JournalTitle    = {Infect. Immun.},
  Date            = {2009},
  DOI             = {10.1128/iai.00272-09},
  Number          = {8},
  Pages           = {3170--3180},
  Volume          = {77}
}

@Article{Salmon2016-kq,
  Author          = {Salmon, Hélène and Idoyaga, Juliana and Rahman, Adeeb
                    and Leboeuf, Marylène and Remark, Romain and Jordan,
                    Stefan and Casanova-Acebes, Maria and Khudoynazarova,
                    Makhzuna and Agudo, Judith and Tung, Navpreet and
                    Chakarov, Svetoslav and Rivera, Christina and Hogstad,
                    Brandon and Bosenberg, Marcus and Hashimoto, Daigo and
                    Gnjatic, Sacha and Bhardwaj, Nina and Palucka, Anna
                    Karolina and Brown, Brian D and Brody, Joshua and
                    Ginhoux, Florent and Merad, Miriam},
  Title           = {Expansion and activation of {{CD103(+})} dendritic cell
                    progenitors at the tumor site enhances tumor responses to
                    therapeutic {PD-L1} and {BRAF} inhibition},
  JournalTitle    = {Immunity},
  Date            = {2016},
  DOI             = {10.1016/j.immuni.2016.03.012},
  Number          = {4},
  Pages           = {924--938},
  Volume          = {44}
}

@Article{volta1987a,
  Author          = {Volta, Umberto and Bonazzi, Claudia and Bianchi,
                    Francesco B. and Baldoni, Anna Maria and Zoli, Marco and
                    Pisi, Emilio},
  Title           = {{IgA} antibodies to dietary antigens in liver
                    cirrhosis},
  JournalTitle    = {Ric Clin Lab},
  Date            = {1987},
  DOI             = {10.1007/bf02912537},
  Number          = {3},
  Pages           = {235--242},
  Volume          = {17}
}

@Article{vonBergen2013,
  Author          = {von Bergen, Martin and Jehmlich, Nico and Taubert,
                    Martin and Vogt, Carsten and Bastida, Felipe and Herbst,
                    Florian-Alexander and Schmidt, Frank and Richnow,
                    Hans-Hermann and Seifert, Jana},
  Title           = {Insights from quantitative metaproteomics and
                    protein-stable isotope probing into microbial ecology},
  JournalTitle    = {ISME J.},
  Date            = {2013},
  DOI             = {10.1038/ismej.2013.78},
  Keywords        = {von Bergen-Selection},
  Number          = {10},
  Pages           = {1877--1885},
  Volume          = {7}
}

@Article{weigert2022a,
  Author          = {Weigert Muñoz, Angela and Hoyer, Elisabeth and
                    Schumacher, Kilian and Grognot, Marianne and Taute, Katja
                    M. and Hacker, Stephan M. and Sieber, Stephan A. and
                    Jung, Kirsten},
  Title           = {Eukaryotic catecholamine hormones influence the
                    chemotactic control of \textit{Vibrio campbellii} by
                    binding to the coupling protein {CheW}},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2022},
  DOI             = {10.1073/pnas.2118227119},
  Keywords        = {Grognot-Selection},
  Number          = {10},
  Volume          = {119}
}

@Article{werkhoven2021a,
  Author          = {Werkhoven, C.H. and Ducher, A. and Berkell, M. and
                    Mysara, M. and Lammens, C. and Torre-Cisneros, J. and
                    Rodríguez-Baño, J. and Herghea, D. and Cornely, O.A.
                    and Biehl, L.M. and Bernard, L. and Dominguez-Luzon, M.A.
                    and Maraki, S. and Barraud, O. and Nica, M. and Jazmati,
                    N. and Sablier-Gallis, F. and Gunzburg, J. and Mentré,
                    F. and Malhotra-Kumar, S. and Bonten, M.J.M. and
                    Vehreschild, M. J. G. T.},
  Title           = {Incidence and predictive biomarkers of Clostridioides
                    difficile infection in hospitalized patients receiving
                    broad-spectrum antibiotics},
  JournalTitle    = {Nat. Commun.},
  Date            = {2021},
  DOI             = {10.1038/s41467-021-22269-y},
  Keywords        = {Vehreschild-Selection},
  Number          = {1},
  Volume          = {12}
}

@Article{wiest2017a,
  Author          = {Wiest, Reiner and Albillos, Agustin and Trauner, Michael
                    and Bajaj, Jasmohan S. and Jalan, Rajiv},
  Title           = {Targeting the gut-liver axis in liver disease},
  JournalTitle    = {J. Hepatol.},
  Date            = {2017},
  DOI             = {10.1016/j.jhep.2017.05.007},
  Number          = {5},
  Pages           = {1084--1103},
  Volume          = {67}
}

@Article{wilkinson_fair_2016,
  Author          = {Wilkinson, Mark D. and others},
  Title           = {The {FAIR} Guiding Principles for scientific data
                    management and stewardship},
  JournalTitle    = {Scientific Data},
  Date            = {2016-12},
  DOI             = {10.1038/sdata.2016.18},
  Keywords        = {{FAIR}},
  langid          = {english},
  Number          = {1},
  Pages           = {160018},
  ShortJournal    = {Sci Data},
  URLDate         = {2021-05-31},
  Volume          = {3}
}

@Article{willing2010a,
  Author          = {Willing, Ben P. and Dicksved, Johan and Halfvarson,
                    Jonas and Andersson, Anders F. and Lucio, Marianna and
                    Zheng, Zongli and Järnerot, Gunnar and Tysk, Curt and
                    Jansson, Janet K. and Engstrand, Lars},
  Title           = {A Pyrosequencing Study in Twins Shows That
                    Gastrointestinal Microbial Profiles Vary With
                    Inflammatory Bowel Disease Phenotypes},
  JournalTitle    = {Gastroenterology},
  Date            = {2010},
  DOI             = {10.1053/j.gastro.2010.08.049},
  Number          = {6},
  Pages           = {1844--1854.e1},
  Volume          = {139}
}

@Article{willmann2019a,
  Author          = {Willmann, Matthias and Vehreschild, Maria J. G. T. and
                    Biehl, Lena M. and Vogel, Wichard and Dörfel, Daniela
                    and Hamprecht, Axel and Seifert, Harald and Autenrieth,
                    Ingo B. and Peter, Silke},
  Title           = {Distinct impact of antibiotics on the gut microbiome and
                    resistome: {A} longitudinal multicenter cohort study},
  JournalTitle    = {BMC Biol.},
  Date            = {2019},
  DOI             = {10.1186/s12915-019-0692-y},
  Keywords        = {Vehreschild-Selection},
  Number          = {1},
  Volume          = {17}
}

@Article{wirtz2019a,
  Author          = {Wirtz, T. H. and Fischer, P. and Backhaus, C. and
                    Bergmann, I. and Brandt, E.F. and Heinrichs, D. and
                    Koenen, M.T. and Schneider, K. M. and Eggermann, T. and
                    Kurth, I. and Stoppe, C. and Bernhagen, J. and Bruns, T.
                    and Fischer, J. and Berg, T. and Trautwein, C. and
                    Berres, M. L.},
  Title           = {Genetic Variants in the Promoter Region of the
                    Macrophage Migration Inhibitory Factor are Associated
                    with the Severity of Hepatitis C Virus-Induced Liver
                    Fibrosis},
  JournalTitle    = {Int. J. Mol. Sci.},
  Date            = {2019},
  DOI             = {10.3390/ijms20153753},
  Keywords        = {Wirtz-Selection},
  Number          = {15},
  Pages           = {3753},
  Volume          = {20}
}

@Article{wirtz2021c,
  Author          = {Wirtz, Theresa H. and Loosen, Sven H. and Schulze-Hagen,
                    Max and Gorgulho, Joao and Kandler, Jennis and Joerdens,
                    Markus and Demir, Münevver and Mohr, Raphael and
                    Bruners, Philipp and Kuhl, Christiane and Trautwein,
                    Christian and Berres, Marie-Luise and Tacke, Frank and
                    Luedde, Tom and Roderburg, Christoph},
  Title           = {Macrophage migration inhibitory factor predicts an
                    unfavorable outcome after transarterial chemoembolization
                    for hepatic malignancies},
  JournalTitle    = {Clin. Transl. Sci.},
  Date            = {2021},
  DOI             = {10.1111/cts.13033},
  ids             = {Wirtz2021-yb},
  Addendum        = preliminarywork,
  Keywords        = {Wirtz-Selection},
  Number          = {5},
  Pages           = {1853--1863},
  Volume          = {14}
}

@Article{wirtz2021e,
  Author          = {Wirtz, Theresa H. and Loosen, Sven H. and Schulze-Hagen,
                    Maximilian and Weiskirchen, Ralf and Buendgens, Lukas and
                    Abu Jhaisha, Samira and Brozat, Jonathan F. and Puengel,
                    Tobias and Vucur, Mihael and Paffenholz, Pia and Kuhl,
                    Christiane and Tacke, Frank and Trautwein, Christian and
                    Luedde, Tom and Roderburg, Christoph and Koch,
                    Alexander},
  Title           = {{CT}-based determination of excessive visceral adipose
                    tissue is associated with an impaired survival in
                    critically ill patients},
  JournalTitle    = {PLoS One},
  Date            = {2021},
  DOI             = {10.1371/journal.pone.0250321},
  ids             = {Wirtz2021-zu},
  Keywords        = {Wirtz-Selection},
  Number          = {4},
  Addendum        = preliminarywork,
  Pages           = {e0250321},
  Volume          = {16}
}

@Article{yue2011a,
  Author          = {Yue, Xiaojing and Izcue, Ana and Borggrefe, Tilman},
  Title           = {Essential role of Mediator subunit Med1 in invariant
                    natural killer T-cell development},
  JournalTitle    = {Proc. Natl. Acad. Sci.},
  Date            = {2011},
  DOI             = {10.1073/pnas.1109095108},
  Keywords        = {Izcue-Selection},
  Number          = {41},
  Pages           = {17105--17110},
  Volume          = {108}
}

@Article{zhu2013a,
  Author          = {Zhu, Lixin and Baker, Susan S. and Gill, Chelsea and
                    Liu, Wensheng and Alkhouri, Razan and Baker, Robert D.
                    and Gill, Steven R.},
  Title           = {Characterization of gut microbiomes in nonalcoholic
                    steatohepatitis {(NASH)} patients: {A} connection between
                    endogenous alcohol and {NASH}},
  JournalTitle    = {Hepatology},
  Date            = {2013},
  DOI             = {10.1002/hep.26093},
  Number          = {2},
  Pages           = {601--609},
  Volume          = {57}
}

@Article{Liu2022,
  Author          = {Liu, Xin and Yao, Jiacheng and Zhao, Yongshan and Wang,
                    Jianbin and Qi, Hai},
  Title           = {Heterogeneous plasma cells and long-lived subsets in
                    response to immunization, autoantigen and microbiota},
  JournalTitle    = {Nat. Immunol.},
  Date            = {2022},
  DOI             = {10.1038/s41590-022-01345-5}
}
