Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

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

(2013) Jiang Zhu et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

(2013) J. M. Simon et al.   GENOME RESEARCH

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity

(2013) B. Zhang et al.   GENOME RESEARCH

Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers

(2013) Justin Malin et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

(2013) Suhn Kyong Rhie et al.   PLoS One

Role of p63 and the Notch pathway in cochlea development and sensorineural deafness

(2013) A. Terrinoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

An enhancer from the 8q24 prostate cancer risk region is sufficient to direct reporter gene expression to a subset of prostate stem-like epithelial cells in transgenic mice

(2012) M.-C. Ting et al.   Disease Models & Mechanisms

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

(2012) Housheng Hansen He et al.   GENOME RESEARCH

The Chromatin Fingerprint of Gene Enhancer Elements

(2012) Gabriel E. Zentner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ENCODE explained

(2012) Joseph R. Ecker et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

In vivo genome editing using a high-efficiency TALEN system

(2012) Victoria M. Bedell et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Evidence for Phenotypic Plasticity in Aggressive Triple-Negative Breast Cancer: Human Biology Is Recapitulated by a Novel Model System

(2012) Nicholas C. D’Amato et al.   PLoS One

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

(2011) Phillippa C. Taberlay et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

Bone morphogenetic protein 4 (BMP4) is required for migration and invasion of breast cancer

(2011) Dan Guo et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

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

(2011) Jason Ernst et al.   NATURE

Polycomb group proteins: repression in 3D

(2011) Frédéric Bantignies et al.   TRENDS IN GENETICS

Optical Redox Ratio Differentiates Breast Cancer Cell Lines Based on Estrogen Receptor Status

(2010) Julie Hanson Ostrander et al.   CANCER RESEARCH

Bone Morphogenetic Proteins: A critical review

(2010) Beth Bragdon et al.   CELLULAR SIGNALLING

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

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

ERα signaling through slug regulates E-cadherin and EMT

(2010) Y Ye et al.   ONCOGENE

Telomerase-immortalized human mammary stem/progenitor cells with ability to self-renew and differentiate

(2010) X. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins

(2010) J. R. A. Hutchins et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

p63 Suppresses Non-epidermal Lineage Markers in a Bone Morphogenetic Protein-dependent Manner via Repression of Smad7

(2009) Laura De Rosa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mammary development meets cancer genomics

(2009) Aleix Prat et al.   NATURE MEDICINE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

(2009) Li Jia et al.   PLoS Genetics

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

(2008) A. P. Fejes et al.   BIOINFORMATICS

The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells

(2008) Sendurai A. Mani et al.   CELL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Generation of Breast Cancer Stem Cells through Epithelial-Mesenchymal Transition

(2008) Anne-Pierre Morel et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY