Epigenomic Landscape of Human Fetal Brain, Heart, and Liver

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Chromatin state dynamics during blood formation

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

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

(2014) Han Wu et al.   PLoS Genetics

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

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

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures

(2013) Jia-Hui Ng et al.   DEVELOPMENTAL CELL

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo

(2013) Michael Sachs et al.   Cell Reports

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

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

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

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

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

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

(2012) Cole Trapnell et al.   Nature Protocols

Cell Fate Potential of Human Pluripotent Stem Cells Is Encoded by Histone Modifications

(2011) Seok-Ho Hong et al.   Cell Stem Cell

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem 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

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

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

(2010) Mazhar Adli et al.   NATURE METHODS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

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