Discovering transcription factor regulatory targets using gene expression and binding data

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

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

(2011) Jason Ernst et al.   NATURE

Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2

(2011) Malay Mandal et al.   NATURE IMMUNOLOGY

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

(2010) Michael P. Verzi et al.   DEVELOPMENTAL CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer

(2009) Sujun Hua et al.   CELL

Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy

(2009) Tohru Fujiwara et al.   MOLECULAR CELL

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression

(2008) Sujun Hua et al.   Molecular Systems Biology

Structure and function of a transcriptional network activated by the MAPK Hog1

(2008) Andrew P Capaldi et al.   NATURE GENETICS

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS