A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

DistanceScan: a tool for promoter modeling

(2010) Vladimir Shelest et al.   BIOINFORMATICS

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

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

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction

(2010) Amaya Ortiz-Barahona et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Association of Hypoxia-inducible Factor (HIF)-1α and HIF-2α DNA Binding with Expression Profiling of Hypoxia-inducible Transcripts

(2009) David R. Mole et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

(2009) Ken Daigoro Yokoyama et al.   NUCLEIC ACIDS RESEARCH

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2009) Hideya Kawaji et al.   GENOME BIOLOGY

Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia

(2009) Xiaobo Xia et al.   GENOME BIOLOGY