Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

Theoretical and empirical quality assessment of transcription factor-binding motifs

(2011) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

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

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Quantifying the effect of sequence variation on regulatory interactions

(2010) Thomas Manke et al.   HUMAN MUTATION

Selective Glucocorticoid Receptor modulators

(2010) Karolien De Bosscher   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters

(2010) Hans-Jörg Warnatz et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

(2009) A. L. Hufton et al.   GENOME RESEARCH

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis

(2009) Arne S. Schaefer et al.   HUMAN MOLECULAR GENETICS

Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression

(2009) Christine Stritt et al.   NATURE NEUROSCIENCE

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

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

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

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

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

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences

(2008) Matthieu Defrance et al.   Nature Protocols

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions

(2008) Thomas Manke et al.   PLoS Computational Biology