Xavier RJ, Podolsky DK, (2007) Unravelling the pathogenesis of inflammatory bowel disease. Nature 448: 427-434.
Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, et al. (2011) Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 43: 246-252.
Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, et al. (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491: 119-124.
Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314: 1461-1463.
Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, et al. (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 39: 596-604.
Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, et al. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nature Genetics 39: 207-211.
Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, et al. (2011) Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 43: 1066-1073.
McGovern DP, Gardet A, Torkvist L, Goyette P, Essers J, et al. (2010) Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 42: 332-337.
Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40: 955-962.
Festen EA, Goyette P, Scott R, Annese V, Zhernakova A, et al. (2009) Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis. Gut 58: 799-804.
Momozawa Y, Mni M, Nakamura K, Coppieters W, Almer S, et al. (2011) Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nat Genet 43: 43-47.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
Williams IR, (2004) Chemokine receptors and leukocyte trafficking in the mucosal immune system. Immunol Res 29: 283-292.
Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, et al. (2007) Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448: 470-473.
Natoli G, Chiocca S, (2008) Nuclear ubiquitin ligases, NF-kappaB degradation, and the control of inflammation. Science signaling 1: pe1.
Zhao W, Wang L, Zhang M, Yuan C, Gao C, (2012) E3 Ubiquitin Ligase Tripartite Motif 38 Negatively Regulates TLR-Mediated Immune Responses by Proteasomal Degradation of TNF Receptor-Associated Factor 6 in Macrophages. J Immunol 188: 2567-2574.
Jin W, Chang M, Sun SC, (2012) Peli: a family of signal-responsive E3 ubiquitin ligases mediating TLR signaling and T-cell tolerance. Cell Mol Immunol 9: 113-122.
Fernandez MI, Regnault B, Mulet C, Tanguy M, Jay P, et al. (2008) Maturation of paneth cells induces the refractory state of newborn mice to Shigella infection. J Immunol 180: 4924-4930.
Li X, Madison BB, Zacharias W, Kolterud A, States D, et al. (2007) Deconvoluting the intestine: molecular evidence for a major role of the mesenchyme in the modulation of signaling cross talk. Physiol Genomics 29: 290-301.
Boyd M, Bressendorff S, Moller J, Olsen J, Troelsen JT, (2009) Mapping of HNF4alpha target genes in intestinal epithelial cells. BMC Gastroenterol 9: 68.
Fang B, Mane-Padros D, Bolotin E, Jiang T, Sladek FM, (2012) Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors. Nucleic Acids Res 40: 5343-5356.
Ktistaki E, Talianidis I, (1997) Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science 277: 109-112.
Kyrmizi I, Hatzis P, Katrakili N, Tronche F, Gonzalez FJ, et al. (2006) Plasticity and expanding complexity of the hepatic transcription factor network during liver development. Genes Dev 20: 2293-2305.
Tomaru Y, Nakanishi M, Miura H, Kimura Y, Ohkawa H, et al. (2009) Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Nucleic Acids Res 37: 1049-1060.
Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, et al. (2010) A human MAP kinase interactome. Nat Methods 7: 801-805.
Das D, Nahle Z, Zhang MQ, (2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol 2: 2006 0029.
Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, et al. (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381.
Garrison WD, Battle MA, Yang C, Kaestner KH, Sladek FM, et al. (2006) Hepatocyte nuclear factor 4alpha is essential for embryonic development of the mouse colon. Gastroenterology 130: 1207-1220.
Darsigny M, Babeu JP, Dupuis AA, Furth EE, Seidman EG, et al. (2009) Loss of hepatocyte-nuclear-factor-4alpha affects colonic ion transport and causes chronic inflammation resembling inflammatory bowel disease in mice. PLoS One 4: e7609.
Marcil V, Seidman E, Sinnett D, Boudreau F, Gendron FP, et al. (2010) Modification in oxidative stress, inflammation, and lipoprotein assembly in response to hepatocyte nuclear factor 4alpha knockdown in intestinal epithelial cells. J Biol Chem 285: 40448-40460.
Goyette P, Lefebvre C, Ng A, Brant SR, Cho JH, et al. (2008) Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis. Mucosal Immunol 1: 131-138.
Asano K, Matsushita T, Umeno J, Hosono N, Takahashi A, et al. (2009) A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nat Genet 41: 1325-1329.
Dassopoulos T, Nguyen GC, Bitton A, Bromfield GP, Schumm LP, et al. (2007) Assessment of reliability and validity of IBD phenotyping within the National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK) IBD Genetics Consortium (IBDGC). Inflamm Bowel Dis 13: 975-983.
Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, et al. (2008) Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Nat Genet 40: 710-712.
Brown AM, Lo KS, Guelpa P, Beaudoin M, Rioux JD, et al. (2010) Optimus Primer: A PCR enrichment primer design program for next-generation sequencing of human exonic regions. BMC Res Notes 3: 185.
Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27: 182-189.
Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
Caja L, Bertran E, Campbell J, Fausto N, Fabregat I, (2011) The transforming growth factor-beta (TGF-beta) mediates acquisition of a mesenchymal stem cell-like phenotype in human liver cells. J Cell Physiol 226: 1214-1223.
Hong MH, Chou YC, Wu YC, Tsai KN, Hu CP, et al. (2012) Transforming growth factor-beta1 suppresses hepatitis B virus replication by the reduction of hepatocyte nuclear factor-4alpha expression. PLoS One 7: e30360.
Wang B, Cai SR, Gao C, Sladek FM, Ponder KP, (2001) Lipopolysaccharide results in a marked decrease in hepatocyte nuclear factor 4 alpha in rat liver. Hepatology 34: 979-989.
Boyd M, Hansen M, Jensen TG, Perearnau A, Olsen AK, et al. (2010) Genome-wide analysis of CDX2 binding in intestinal epithelial cells (Caco-2). J Biol Chem 285: 25115-25125.
McKinney-Freeman SL, Lengerke C, Jang IH, Schmitt S, Wang Y, et al. (2008) Modulation of murine embryonic stem cell-derived CD41+c-kit+ hematopoietic progenitors by ectopic expression of Cdx genes. Blood 111: 4944-4953.
