Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Shape-based peak identification for ChIP-Seq

(2011) Valerie Hower et al.   BMC BIOINFORMATICS

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data

(2011) Brandon M. Malone et al.   PLoS One

VDA, a Method of Choosing a Better Algorithm with Fewer Validations

(2011) Francesco Strino et al.   PLoS One

Genome-wide remodeling of the epigenetic landscape during myogenic differentiation

(2011) P. Asp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Xun Lan et al.   BIOINFORMATICS

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

A CTCF-independent role for cohesin in tissue-specific transcription

(2010) D. Schmidt et al.   GENOME RESEARCH

The Mammalian Sin3 Proteins Are Required for Muscle Development and Sarcomere Specification

(2010) C. van Oevelen et al.   MOLECULAR AND CELLULAR BIOLOGY

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs

(2010) Morten Beck Rye et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

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

(2009) Chongzhi Zang et al.   BIOINFORMATICS

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou et al.   BMC BIOINFORMATICS

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

E2f3b plays an essential role in myogenic differentiation through isoform-specific gene regulation

(2009) P. Asp et al.   GENES & DEVELOPMENT

Genomic location analysis by ChIP-Seq

(2009) Artem Barski et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

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

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

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

(2008) Han Xu et al.   BIOINFORMATICS

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

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

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

(2008) Anton Valouev et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY