The large collections of ChIP-seq data rapidly accumulating in public data warehouses
provide genome-wide binding site maps for hundreds of transcription factors (TFs) …

With this latest release of ReMap (http://remap. cisreg. eu), we present a unique collection of
regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq …

Background The global effort to annotate the non-coding portion of the human genome
relies heavily on chromatin immunoprecipitation data generated with high-throughput DNA …

The increasing volume of ChIP-chip and ChIP-seq data being generated creates a
challenge for standard, integrative and reproducible bioinformatics data analysis platforms …

Next-generation sequencing is revolutionizing the identification of transcription factor
binding sites throughout the human genome. However, the bioinformatics analysis of large …

The availability of omic data produced from international consortia, as well as from
worldwide laboratories, is offering the possibility both to answer long-standing questions in …

Motivation: Biological analysis has shifted from identifying genes and transcripts to mapping
these genes and transcripts to biological functions. The ENCODE Project has generated …

Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data.
Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene …

Transcription is regulated by transcription factor (TF) binding at promoters and distal
regulatory elements and histone modifications that control the accessibility of these …

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is
rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array …