Background Unraveling the mechanisms that regulate gene expression is a major challenge
in biology. An important task in this challenge is to identify regulatory elements, especially …

Microorganisms in most ecological niches are constantly exposed to variations of many
environmental factors, including temperature; oxygen, nutrient, and water availability; …

Identification of genomic regulatory elements is essential for understanding the dynamics of
cellular processes. This task has been substantially facilitated by the availability of genome …

Motivation: Probabilistic approaches for inferring transcription factor binding sites (TFBSs)
and regulatory motifs from DNA sequences have been developed for over two decades …

Transcription initiation, essential to gene expression regulation, involves recruitment of
basal transcription factors to the core promoter elements (CPEs). The distribution of currently …

Transcription factors are proteins that bind to specific DNA sequences and play important
roles in controlling the expression levels of their target genes. Hence, prediction of …

Background A key problem in the sequence-based reconstruction of regulatory networks in
bacteria is the lack of specificity in operator predictions. The problem is especially prominent …

We present a new algorithm, BOBRO, for prediction of cis-regulatory motifs in a given set of
promoter sequences. The algorithm substantially improves the prediction accuracy and …

Background Phylogenetic footprinting is an important computational technique for identifying
cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend …

The discovery of gene regulatory elements requires the synergism between computational
and experimental techniques in order to reveal the underlying regulatory mechanisms that …