Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles

Integrative analysis of 111 reference human epigenomes

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HTSeq--a Python framework to work with high-throughput sequencing data

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Comprehensive molecular characterization of urothelial bladder carcinoma

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deepTools: a flexible platform for exploring deep-sequencing data

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RUNX1, a transcription factor mutated in breast cancer, controls the fate of ER-positive mammary luminal cells

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Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Lessons from the Cancer Genome

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The Chromatin Fingerprint of Gene Enhancer Elements

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Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst 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

H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites

(2012) Dheepa Balasubramanian et al.   Genome Medicine

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Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

The Nuclear Receptor Nr5a2 Can Replace Oct4 in the Reprogramming of Murine Somatic Cells to Pluripotent Cells

(2010) Jian-Chien Dominic Heng et al.   Cell Stem Cell

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

Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

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

TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

EsrrbActivatesOct4Transcription and Sustains Self-renewal and Pluripotency in Embryonic Stem Cells

(2008) Xiaofei Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-Wide Pattern of TCF7L2/TCF4 Chromatin Occupancy in Colorectal Cancer Cells

(2008) P. Hatzis et al.   MOLECULAR AND CELLULAR BIOLOGY

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors

(2008) Ittai Ben-Porath et al.   NATURE GENETICS