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

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

(2010) Ming Hu et al.   NUCLEIC ACIDS RESEARCH

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

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

(2009) Ivan V. Kulakovskiy et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function

(2009) Noëlle Guillon et al.   PLoS One

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

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

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

(2008) Xi Chen et al.   CELL

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS