Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells

Identification, visualization and clonal analysis of intestinal stem cells in fish

(2016) Narges Aghaallaei et al.   DEVELOPMENT

Microbiota-induced obesity requires farnesoid X receptor

(2016) Ava Parséus et al.   GUT

Stem vs non-stem cell origin of colorectal cancer

(2015) D J Huels et al.   BRITISH JOURNAL OF CANCER

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Glucose Tolerance Is Improved in Mice Invalidated for the Nuclear Receptor HNF-4γ: A Critical Role for Enteroendocrine Cell Lineage

(2015) Floriane Baraille et al.   DIABETES

Epithelial-specific ETS-1 (ESE1/ELF3) regulates apoptosis of intestinal epithelial cells in ulcerative colitis via accelerating NF-κB activation

(2015) Liren Li et al.   IMMUNOLOGIC RESEARCH

MicroRNAs Classify Different Disease Behavior Phenotypes of Crohnʼs Disease and May Have Prognostic Utility

(2015) Bailey C. E. Peck et al.   INFLAMMATORY BOWEL DISEASES

The evolving roles of canonical WNT signaling in stem cells and tumorigenesis: implications in targeted cancer therapies

(2015) Ke Yang et al.   LABORATORY INVESTIGATION

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Developmental regulation of apical endocytosis controls epithelial patterning in vertebrate tubular organs

(2015) Alejo E. Rodríguez-Fraticelli et al.   NATURE CELL BIOLOGY

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Distinct Processes and Transcriptional Targets Underlie CDX2 Requirements in Intestinal Stem Cells and Differentiated Villus Cells

(2015) Adrianna K. San Roman et al.   Stem Cell Reports

GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of histone H3, lysine 27

(2014) B.E. Aronson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Dynamic expression and roles of Hes factors in neural development

(2014) Ryoichiro Kageyama et al.   CELL AND TISSUE RESEARCH

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

(2014) J. Gray Camp et al.   GENOME RESEARCH

Opposite Effects of Interferon Regulatory Factor 1 and Osteopontin on the Apoptosis of Epithelial Cells Induced by TNF-α in Inflammatory Bowel Disease

(2014) Ruihan Tang et al.   INFLAMMATORY BOWEL DISEASES

Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction with Transcription Factor CDX2

(2014) Adrianna K. San Roman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Intestinal transport and metabolism of bile acids

(2014) Paul A. Dawson et al.   JOURNAL OF LIPID RESEARCH

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

Intestinal epithelial MyD88 is a sensor switching host metabolism towards obesity according to nutritional status

(2014) Amandine Everard et al.   Nature Communications

Hes1 is involved in the self-renewal and tumourigenicity of stem-like cancer cells in colon cancer

(2014) Fei Gao et al.   Scientific Reports

The Role of Gut Hormone Peptide YY in Energy and Glucose Homeostasis: Twelve Years On

(2013) Sean Manning et al.   Annual Review of Physiology

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Homeostasis in Intestinal Epithelium Is Orchestrated by the Circadian Clock and Microbiota Cues Transduced by TLRs

(2013) Atish Mukherji et al.   CELL

Wnt signaling in adult intestinal stem cells and cancer

(2013) Michaela Krausova et al.   CELLULAR SIGNALLING

Mucosal Immunology of Food Allergy

(2013) M. Cecilia Berin et al.   CURRENT BIOLOGY

Conserved non-coding elements and cis regulation: actions speak louder than words

(2013) A. C. Nelson et al.   DEVELOPMENT

Deletion of Intestinal Epithelial Cell STAT3 Promotes T-Lymphocyte STAT3 Activation and Chronic Colitis Following Acute Dextran Sodium Sulfate Injury in Mice

(2013) Tara A. Willson et al.   INFLAMMATORY BOWEL DISEASES

Genomic organization and transcription of the medaka and zebrafish cellular retinol-binding protein (rbp) genes

(2013) Manoj B. Parmar et al.   Marine Genomics

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis

(2013) Theresa Alenghat et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

T cell development requires constraint of the myeloid regulator C/EBP-α by the Notch target and transcriptional repressor Hes1

(2013) Maria Elena De Obaldia et al.   NATURE IMMUNOLOGY

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

(2013) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Bacteria Regulate Intestinal Epithelial Cell Differentiation Factors Both In Vitro and In Vivo

(2013) Svetlana Becker et al.   PLoS One

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Transgenic Overexpression of cdx1b Induces Metaplastic Changes of Gene Expression in Zebrafish Esophageal Squamous Epithelium

(2013) Bo Hu et al.   Zebrafish

Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications

(2012) Jianguo Lu et al.   BMC GENOMICS

Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish

(2012) Ivana Semova et al.   Cell Host & Microbe

RETRACTED: Visualization of lipid metabolism in the zebrafish intestine reveals a relationship between NPC1L1-mediated cholesterol uptake and dietary fatty acid

(2012) James W. Walters et al.   CHEMISTRY & BIOLOGY

The metalloproteinase inhibitor Reck is essential for zebrafish DRG development

(2012) A. Prendergast et al.   DEVELOPMENT

The role of Hes genes in intestinal development, homeostasis and tumor formation

(2012) T. Ueo et al.   DEVELOPMENT

Stem cells and lineages of the intestine: a developmental and evolutionary perspective

(2012) Shigeo Takashima et al.   DEVELOPMENT GENES AND EVOLUTION

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding

(2012) M. P. Verzi et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The Ileal Lipid Binding Protein Is Required for Efficient Absorption and Transport of Bile Acids in the Distal Portion of the Murine Small Intestine

(2012) Dana Praslickova et al.   PLoS One

Role of Smad7 in inflammatory bowel diseases

(2012) Giovanni Monteleone   WORLD JOURNAL OF GASTROENTEROLOGY

Transcriptional Networks in Liver and Intestinal Development

(2012) K. L. Sheaffer et al.   Cold Spring Harbor Perspectives in Biology

Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription

(2012) J. Gray Camp et al.   PLoS Genetics

Current and emerging approaches to define intestinal epithelium-specific transcriptional networks

(2011) Anders Krüger Olsen et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Origin of the brush cell lineage in the mouse intestinal epithelium

(2011) Matthew Bjerknes et al.   DEVELOPMENTAL BIOLOGY

Intestinal development and differentiation

(2011) Taeko K. Noah et al.   EXPERIMENTAL CELL RESEARCH

Microbial Colonization Induces Dynamic Temporal and Spatial Patterns of NF-κB Activation in the Zebrafish Digestive Tract

(2011) Michelle Kanther et al.   GASTROENTEROLOGY

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

(2011) Erik Larsson et al.   GUT

DDR1 Receptor Tyrosine Kinase Promotes Prosurvival Pathway through Notch1 Activation

(2011) Hyung-Gu Kim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Novelcis-Regulatory Modules Control Expression of the Hairy and Enhancer of Split-1 (HES1) Transcription Factor in Myoblasts

(2011) Danuta M. Jeziorska et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Wnt signaling specifies and patterns intestinal endoderm

(2011) Richard I. Sherwood et al.   MECHANISMS OF DEVELOPMENT

Notch Lineages and Activity in Intestinal Stem Cells Determined by a New Set of Knock-In Mice

(2011) Silvia Fre et al.   PLoS One

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine

(2010) Zhengyuan Wang et al.   BMC GENOMICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88

(2010) S. E. Cheesman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

(2009) Nan Gao et al.   DEVELOPMENTAL CELL

Notch-responsive cells initiate the secondary transition in larval zebrafish pancreas

(2009) Michael J. Parsons et al.   MECHANISMS OF DEVELOPMENT

Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

hnRNP I Inhibits Notch Signaling and Regulates Intestinal Epithelial Homeostasis in the Zebrafish

(2009) Jing Yang et al.   PLoS Genetics

Spatio-temporal distribution of fatty acid-binding protein 6 (fabp6) gene transcripts in the developing and adult zebrafish (Danio rerio)

(2008) Fernanda A. Alves-Costa et al.   FEBS Journal

Enteric infection meets intestinal function: how bacterial pathogens cause diarrhoea

(2008) V. K. Viswanathan et al.   NATURE REVIEWS MICROBIOLOGY

Malnutrition as an enteric infectious disease with long-term effects on child development

(2008) Richard L Guerrant et al.   NUTRITION REVIEWS

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

(2007) D. M. McGaughey et al.   GENOME RESEARCH