PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors

(2013) J. D. Fleming et al.   GENOME RESEARCH

Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions

(2013) Andrew Paul Hutchins et al.   NUCLEIC ACIDS RESEARCH

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

(2012) Federico Zambelli et al.   BRIEFINGS IN BIOINFORMATICS

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

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

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

(2011) B.-K. Lee et al.   GENOME RESEARCH

CENTDIST: discovery of co-associated factors by motif distribution

(2011) Zhizhuo Zhang et al.   NUCLEIC ACIDS RESEARCH

Inferring transcription factor complexes from ChIP-seq data

(2011) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

(2008) Matthew S Hestand et al.   BMC BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

A role for Myc in facilitating transcription activation by E2F1

(2008) J Y Leung et al.   ONCOGENE