Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

(2020) Neil McCarthy et al.   Cell Stem Cell

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

(2019) Jelena Petrovic et al.   MOLECULAR CELL

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

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

(2019) Lei Chen et al.   NATURE GENETICS

HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine

(2019) Lei Chen et al.   DEVELOPMENT

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

(2019) Judhajeet Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HNF4 Regulates Fatty Acid Oxidation and is Required for Renewal of Intestinal Stem Cells in Mice

(2019) Lei Chen et al.   GASTROENTEROLOGY

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

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

(2018) Caleb A Lareau et al.   NATURE METHODS

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

(2018) Noelia Díaz et al.   Nature Communications

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

(2017) Madhurima Saxena et al.   GENES & DEVELOPMENT

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

(2017) James M. Davison et al.   GENOME RESEARCH

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

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

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

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

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

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

The limitations of simple gene set enrichment analysis assuming gene independence

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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