A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data

(2011) Fei Gu et al.   BMC Systems Biology

A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer

(2011) Changyu Shen et al.   BMC Systems Biology

Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells

(2011) Benjamin A.T. Rodriguez et al.   CARCINOGENESIS

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

(2011) Jason Ernst et al.   NATURE

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data

(2010) Xun Lan et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

(2010) Zhaohui S Qin et al.   BMC BIOINFORMATICS

Reversibility of pre-malignant estrogen-induced epigenetic changes

(2010) Kristy Kutanzi et al.   CELL CYCLE

Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping

(2010) P.-Y. Hsu et al.   GENOME RESEARCH

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

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

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

(2008) Han Xu et al.   BIOINFORMATICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH