Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps

(2015) Manu Setty et al.   PLoS Computational Biology

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Long range regulation of the sonic hedgehog gene

(2014) Eve Anderson et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

The chromatin landscape and transcription factors in T cell programming

(2014) Ellen V. Rothenberg   TRENDS IN IMMUNOLOGY

Transcriptional regulation of the Ikzf1 locus

(2013) T. Yoshida et al.   BLOOD

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

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

Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers

(2013) Justin Malin et al.   NUCLEIC ACIDS RESEARCH

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers

(2013) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

(2012) Yin Shen et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Chromatin "Prepattern" and Histone Modifiers in a Fate Choice for Liver and Pancreas

(2011) C.-R. Xu et al.   SCIENCE

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Pioneer factors in embryonic stem cells and differentiation

(2010) Stephen T Smale   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate

(2010) Ye Zheng et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY