Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

(2016) Peggy Prickaerts et al.   Epigenetics & Chromatin

Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells

(2016) Ying Liu et al.   Nature Communications

Is this the right normalization? A diagnostic tool for ChIP-seq normalization

(2015) Claudia Angelini et al.   BMC BIOINFORMATICS

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

(2015) Kaifu Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models

(2014) Hans-Ulrich Klein et al.   BIOINFORMATICS

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

(2014) N. Bonhoure et al.   GENOME RESEARCH

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

Cancer genomics identifies disrupted epigenetic genes

(2013) Laia Simó-Riudalbas et al.   HUMAN GENETICS

Normalization of ChIP-seq data with control

(2012) Kun Liang et al.   BMC BIOINFORMATICS

Cancer epigenomics: beyond genomics

(2012) Juan Sandoval et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models

(2011) C. Taslim et al.   BIOINFORMATICS

An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment

(2011) Magnus D Lynch et al.   EMBO JOURNAL

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

Efficiently identifying genome-wide changes with next-generation sequencing data

(2011) Weichun Huang et al.   NUCLEIC ACIDS RESEARCH

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

(2011) Jose M Muiño et al.   Plant Methods

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

(2011) Eloi Mercier et al.   PLoS One

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

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

Generation of bivalent chromatin domains during cell fate decisions

(2011) Marco De Gobbi et al.   Epigenetics & Chromatin

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

Determination of enriched histone modifications in non-genic portions of the human genome

(2009) Jeffrey A Rosenfeld et al.   BMC GENOMICS

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

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

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

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

Global Rank-invariant Set Normalization (GRSN) to reduce systematic distortions in microarray data

(2008) Carl R Pelz et al.   BMC BIOINFORMATICS

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

(2008) David A Nix et al.   BMC BIOINFORMATICS

Stem cell regulation by polycomb repressors: postponing commitment

(2008) Alexandra M Pietersen et al.   CURRENT OPINION IN CELL BIOLOGY

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY