ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis

(2011) Xuefeng Fang et al.   BMC GENOMICS

CisGenome Browser: a flexible tool for genomic data visualization

(2010) H. Jiang et al.   BIOINFORMATICS

FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution

(2010) Mulin Jun Li et al.   BIOINFORMATICS

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Direct targets of Klf5 transcription factor contribute to the maintenance of mouse embryonic stem cell undifferentiated state

(2010) Silvia Parisi et al.   BMC BIOLOGY

Uncovering Early Response of Gene Regulatory Networks in ESCs by Systematic Induction of Transcription Factors

(2009) Akira Nishiyama et al.   Cell Stem Cell

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Eukaryotic transcription factor binding sites--modeling and integrative search methods

(2008) S. Hannenhalli   BIOINFORMATICS

Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data

(2008) Alexei A Sharov et al.   BMC GENOMICS

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY