Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation

(2016) C. K. Kaufman et al.   SCIENCE

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity

(2015) Sudhir Thakurela et al.   GENOME RESEARCH

Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice

(2015) Rene C. Adam et al.   NATURE

Super-enhancers delineate disease-associated regulatory nodes in T cells

(2015) Golnaz Vahedi et al.   NATURE

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SEA: a super-enhancer archive

(2015) Yanjun Wei et al.   NUCLEIC ACIDS RESEARCH

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

(2015) Hyung Joo Lee et al.   Nature Communications

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain

(2014) Marit W. Vermunt et al.   Cell Reports

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén 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

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

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

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3

(2013) Joerg Betschinger et al.   CELL

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

(2013) Kerstin Howe et al.   NATURE

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

Evolution of transcriptional enhancers and animal diversity

(2013) M. Rubinstein et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Enhancer turnover and conserved regulatory function in vertebrate evolution

(2013) S. Domene et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Nebula—a web-server for advanced ChIP-seq data analysis

(2012) Valentina Boeva et al.   BIOINFORMATICS

Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway

(2012) Cong Xu et al.   DEVELOPMENTAL CELL

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

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

(2012) Morgane Thomas-Chollier et al.   Nature Protocols

Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells

(2012) Pietro Vella et al.   NUCLEIC ACIDS RESEARCH

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

(2012) Shoa L. Clarke et al.   PLoS Genetics

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events

(2011) D. K. Goode et al.   DEVELOPMENT

Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

(2011) Aaron W. Aday et al.   DEVELOPMENTAL BIOLOGY

Genome-wide identification of conserved regulatory function in diverged sequences

(2011) L. Taher et al.   GENOME RESEARCH

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance

(2010) B. L. Kidder et al.   GENOME RESEARCH

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates

(2010) Ziyang Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2008) Xi Chen et al.   CELL

Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia

(2008) M. G. Guenther et al.   GENES & DEVELOPMENT

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics