LASAGNA: A novel algorithm for transcription factor binding site alignment

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

SiTaR: a novel tool for transcription factor binding site prediction

(2011) Eugen Fazius et al.   BIOINFORMATICS

c-Myb and GATA-3 Cooperatively Regulate IL-13 Expression via Conserved GATA-3 Response Element and Recruit Mixed Lineage Leukemia (MLL) for Histone Modification of the IL-13 Locus

(2011) T. Kozuka et al.   JOURNAL OF IMMUNOLOGY

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

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

Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction

(2010) R. A. Salama et al.   NUCLEIC ACIDS RESEARCH

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction

(2009) Chen Yanover et al.   BIOINFORMATICS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

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

(2008) S. Hannenhalli   BIOINFORMATICS

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols