A reinforcing HNF4–SMAD4 feed-forward module stabilizes enterocyte identity

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements

(2018) Luca Pinello et al.   BIOINFORMATICS

SMAD4 suppresses WNT-driven de-differentiation and oncogenesis in the differentiated gut epithelium

(2018) Ansu O. Perekatt et al.   CANCER RESEARCH

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

(2018) Andreas E. Moor et al.   CELL

Transcription factor-dependent ‘anti-repressive’ mammalian enhancers exclude H3K27me3 from extended genomic domains

(2017) Madhurima Saxena et al.   GENES & DEVELOPMENT

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Hierarchy and Plasticity in the Intestinal Stem Cell Compartment

(2017) Maryam Yousefi et al.   TRENDS IN CELL BIOLOGY

BMP restricts stemness of intestinal Lgr5+ stem cells by directly suppressing their signature genes

(2017) Zhen Qi et al.   Nature Communications

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

(2016) Paul W. Tetteh et al.   Cell Stem Cell

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

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

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

Aberrant epithelial GREM1 expression initiates colonic tumorigenesis from cells outside the stem cell niche

(2014) Hayley Davis et al.   NATURE MEDICINE

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

YY1 is indispensable for Lgr5+ intestinal stem cell renewal

(2014) A. O. Perekatt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

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

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling

(2012) Vivian W. Y. Wong et al.   NATURE CELL BIOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors

(2012) Bin Fang et al.   NUCLEIC ACIDS RESEARCH

The limitations of simple gene set enrichment analysis assuming gene independence

(2012) Pablo Tamayo et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

The Intestinal Stem Cell Signature Identifies Colorectal Cancer Stem Cells and Predicts Disease Relapse

(2011) Anna Merlos-Suárez et al.   Cell Stem Cell

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

(2010) Michael P. Verzi et al.   DEVELOPMENTAL CELL

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

Hepatocyte nuclear factor 4α contributes to an intestinal epithelial phenotype in vitro and plays a partial role in mouse intestinal epithelium differentiation

(2009) Jean-Philippe Babeu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

Hepatocyte Nuclear Factor 4 , a Key Factor for Homeostasis, Cell Architecture, and Barrier Function of the Adult Intestinal Epithelium

(2009) A.-L. Cattin et al.   MOLECULAR AND CELLULAR BIOLOGY

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY