histoneHMM: Differential analysis of histone modifications with broad genomic footprints

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data

(2014) Yanxiao Zhang et al.   BIOINFORMATICS

Natural variation of histone modification and its impact on gene expression in the rat genome

(2014) C. Rintisch et al.   GENOME RESEARCH

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets

(2013) Jianrong Wang et al.   BIOINFORMATICS

Genome-Wide Analysis of Chromatin States Reveals Distinct Mechanisms of Sex-Dependent Gene Regulation in Male and Female Mouse Liver

(2013) A. Sugathan et al.   MOLECULAR AND CELLULAR BIOLOGY

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

A Histone Mutant Reproduces the Phenotype Caused by Loss of Histone-Modifying Factor Polycomb

(2013) A. R. Pengelly et al.   SCIENCE

PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription

(2012) D. B. Beck et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

(2012) Mariann Micsinai et al.   NUCLEIC ACIDS RESEARCH

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Epigenetic changes induced by curcumin and other natural compounds

(2011) Simone Reuter et al.   Genes and Nutrition

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

Regulation of X-chromosome inactivation by the X-inactivation centre

(2011) Sandrine Augui et al.   NATURE REVIEWS GENETICS

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

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

(2010) Zhaohui S Qin et al.   BMC BIOINFORMATICS

Global survey of escape from X inactivation by RNA-sequencing in mouse

(2010) F. Yang et al.   GENOME RESEARCH

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

(2010) S. S. Atanur et al.   GENOME RESEARCH

Differential neonatal testosterone imprinting of GH-dependent liver proteins and genes in female mice

(2010) María Cecilia Ramirez et al.   JOURNAL OF ENDOCRINOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice

(2010) S. Peleg et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Epigenetic histone modifications of human transposable elements: genome defense versus exaptation

(2010) Ahsan Huda et al.   Mobile DNA

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

(2009) Chongzhi Zang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou et al.   BMC BIOINFORMATICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

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

(2008) Han Xu et al.   BIOINFORMATICS

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

The Rat Genome Database 2009: variation, ontologies and pathways

(2008) M. R. Dwinell et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY