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

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

1995 • 93,704 citations

Model-based Analysis of ChIP-Seq (MACS)

2008 • 15,719 citations

The control of the false discovery rate in multiple testing under dependency

2001 • 9,798 citations

High-Resolution Profiling of Histone Methylations in the Human Genome

2007 • 6,479 citations

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

2007 • 3,994 citations

Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain

2001 • 2,768 citations

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

2007 • 2,764 citations

Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins

2001 • 2,746 citations

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

2008 • 2,492 citations

Combinatorial patterns of histone acetylations and methylations in the human genome

2008 • 2,214 citations

The Mammalian Epigenome

2007 • 1,977 citations

Microarray data normalization and transformation

2002 • 1,956 citations

Controlling the double helix

2003 • 1,102 citations

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

2009 • 1,098 citations

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

2008 • 909 citations

Polycomb silencing mechanisms and the management of genomic programmes

2006 • 847 citations

Structure and Function of a Human TAF _II 250 Double Bromodomain Module

2000 • 808 citations

An integrated software system for analyzing ChIP-chip and ChIP-seq data

2008 • 718 citations

A model for transmission of the H3K27me3 epigenetic mark

2008 • 715 citations

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

2008 • 690 citations

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

2009 • 582 citations

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

2009 • 578 citations

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

2009 • 552 citations

Genome-wide identification ofin vivoprotein-DNA binding sites from ChIP-Seq data

2008 • 530 citations

The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p

2000 • 508 citations

Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification

2007 • 438 citations

Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31

1999 • 433 citations

F-Seq: a feature density estimator for high-throughput sequence tags

2008 • 371 citations

Genome-wide approaches to studying chromatin modifications

2008 • 361 citations

Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-γ

2007 • 289 citations

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

2008 • 266 citations

H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

2008 • 237 citations

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

2008 • 223 citations

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

2008 • 185 citations

EZH2 and Histone 3 Trimethyl Lysine 27 Associated with Il4 and Il13 Gene Silencing in TH1 Cells

2005 • 153 citations

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

2008 • 148 citations

GeneTrack—a genomic data processing and visualization framework

2008 • 107 citations

Modeling ChIP Sequencing In Silico with Applications

2008 • 101 citations