RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data

(2010) Mike J. Mason et al.   BIOINFORMATICS

Deep and wide digging for binding motifs in ChIP-Seq data

(2010) I. V. Kulakovskiy et al.   BIOINFORMATICS

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

(2010) Simon J. van Heeringen et al.   BIOINFORMATICS

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

(2010) Ming Hu et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions

(2010) Phaedra Agius et al.   PLoS Computational Biology

Motif discovery and motif finding from genome-mapped DNase footprint data

(2009) Ivan V. Kulakovskiy et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

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

A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data

(2009) Xin He et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Xi Chen et al.   CELL

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY