QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions

Stem-Like Cells with Luminal Progenitor Phenotype Survive Castration in Human Prostate Cancer

(2012) Markus Germann et al.   STEM CELLS

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

(2012) Seth Frietze et al.   GENOME BIOLOGY

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

(2011) C. Taslim et al.   BIOINFORMATICS

Detecting differential binding of transcription factors with ChIP-seq

(2011) Kun Liang et al.   BIOINFORMATICS

Epigenetic Silencing Mediated through Activated PI3K/AKT Signaling in Breast Cancer

(2011) T. Zuo et al.   CANCER RESEARCH

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

ChIP-seq Defined Genome-Wide Map of TGFβ/SMAD4 Targets: Implications with Clinical Outcome of Ovarian Cancer

(2011) Brian A. Kennedy et al.   PLoS One

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

(2010) Xun Lan et al.   BIOINFORMATICS

Gene expression profiling of human breast tissue samples using SAGE-Seq

(2010) Z. J. Wu et al.   GENOME RESEARCH

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263

(2009) Seth Frietze et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Epigenomics and breast cancer

(2008) Pang-Kuo Lo et al.   PHARMACOGENOMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY