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

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

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

(2009) Teemu D Laajala et al.   BMC GENOMICS

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

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Extracting transcription factor targets from ChIP-Seq data

(2009) Geetu Tuteja et al.   NUCLEIC ACIDS RESEARCH

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

(2009) Ola Wallerman et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2008) Xi Chen et al.   CELL

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

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

(2008) Anton Valouev et al.   NATURE METHODS

Genome-wide approaches to studying chromatin modifications

(2008) Dustin E. Schones et al.   NATURE REVIEWS GENETICS

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