ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates

(2018) Emily Goren et al.   BIOINFORMATICS

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

(2016) Lydia Müller et al.   BMC BIOINFORMATICS

Using combined evidence from replicates to evaluate ChIP-seq peaks

(2015) Vahid Jalili et al.   BIOINFORMATICS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Yanxiao Zhang et al.   BIOINFORMATICS

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS

(2014) Yajie Yang et al.   Computational and Structural Biotechnology Journal

The exact probability distribution of the rank product statistics for replicated experiments

(2013) Rob Eisinga et al.   FEBS LETTERS

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Comments on the rank product method for analyzing replicated experiments

(2010) James A. Koziol   FEBS LETTERS

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

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

Repeatability of published microarray gene expression analyses

(2009) John P A Ioannidis et al.   NATURE GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2008) David A Nix et al.   BMC BIOINFORMATICS

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

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