Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

(2014) William C. Gasper et al.   Scientific Reports

Genome-wide analysis of H4K5 acetylation associated with fear memory in mice

(2013) C Park et al.   BMC GENOMICS

BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells

(2013) Diego Chacon et al.   NUCLEIC ACIDS RESEARCH

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

(2013) Qixuan Wang et al.   NUCLEIC ACIDS RESEARCH

SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor

(2013) Ville Paakinaho et al.   NUCLEIC ACIDS RESEARCH

Role of lysine methylation of NF- B in differential gene regulation

(2013) T. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

Sequencing the transcriptional network of androgen receptor in prostate cancer

(2012) Kern Rei Chng et al.   CANCER LETTERS

A transcriptional repressor co-regulatory network governing androgen response in prostate cancers

(2012) Kern Rei Chng et al.   EMBO JOURNAL

High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation

(2012) Angela R. Wu et al.   LAB ON A CHIP

Analysis of the epigenetic status of telomeres by using ChIP-seq data

(2012) María I. Vaquero-Sedas et al.   NUCLEIC ACIDS RESEARCH

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

A chromatin-modifying function of JNK during stem cell differentiation

(2011) Vijay K Tiwari et al.   NATURE GENETICS

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

(2010) W. Niu et al.   GENOME RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY