Recent data have paved the way to mechanistic studies into the role of Tbx1 during
development. Tbx1 is haploinsufficient and is involved in an important genetic disorder. The …

The influx of high-throughput data and the need for complex models to describe the
interaction of prokaryotic transcription factors (TF) with their target sites pose new challenges …

Core promoters are stretches of DNA at the beginning of genes that contain information that
facilitates the binding of transcription initiation complexes. Different functional subsets of …

Background Eukaryotic genome acquires functionality upon proper packaging within the
nucleus. This process is facilitated by the structural framework of Nuclear Matrix, a nucleo …

The binding motifs of many transcription factors (TFs) comprise a higher degree of
complexity than a single position weight matrix model permits. Additional complexity is …

Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput
chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for …

An important question in biology is how different promoter-architectures contribute to the
diversity in regulation of transcription initiation. A step forward has been the production of …

Motivation High-throughput chromatin immunoprecipitation (ChIP) sequencing-based
assays capture genomic regions associated with the profiled transcription factor (TF). ChIP …

High-throughput sequencing-based assays measure different biochemical activities
pertaining to gene regulation, genome-wide. These activities include transcription factor (TF) …

We present THiCweed, a new approach to analyzing transcription factor binding data from
high-throughput chromatin immunoprecipitation-sequencing (ChIP-seq) experiments …