CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

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

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

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Tmod: toolbox of motif discovery

(2009) H. Sun et al.   BIOINFORMATICS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

CUDA–MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units

(2009) Yongchao Liu et al.   PATTERN RECOGNITION LETTERS

Discovery of Regulatory Elements is Improved by a Discriminatory Approach

(2009) Eivind Valen et al.   PLoS Computational 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