Motivation: Computational prediction and analysis of transcription regulatory regions in DNA
sequences has the potential to accelerate greatly our understanding of how cellular …

Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute
cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling …

Identification and annotation of all the functional elements in the genome, including genes
and the regulatory sequences, is a fundamental challenge in genomics and computational …

Motivation: The identification of regulatory control regions within genomes is a major
challenge. Studies have demonstrated that regulating regions can be described as locally …

Given the DNA-binding specificities (motifs) of one or more transcription factors, an important
bioinformatics problem is to discover significant clusters of binding sites for the transcription …

Motivation: In the living cell nucleus, genomic DNA is packaged into chromatin. DNA
sequences that regulate transcription and other chromosomal processes are associated with …

The human genome encodes the transcriptional control of its genes in clusters of cis‐
elements that constitute enhancers, silencers and promoter signals. The sequence motifs of …

The interaction of proteins with DNA recognition motifs regulates a number of fundamental
biological processes, including transcription. To understand these processes, we need to …

Background Cis-regulatory modules are combinations of regulatory elements occurring in
close proximity to each other that control the spatial and temporal expression of genes. The …

In this paper, we propose a functional view on the in silico prediction of transcriptional
regulation. We present a method to predict biological functions regulated by a combinatorial …