Studies of the genetic regulation involved in drug metabolizing enzymes and drug
transporters are of great interest to understand the molecular mechanisms of drug response …

The identification of promoters and their regulatory elements is one of the major challenges
in bioinformatics and integrates comparative, structural, and functional genomics. Many …

Pattern discovery in unaligned DNA sequences is a fundamental problem in computational
biology with important applications in finding regulatory signals. Current approaches to …

This paper introduces two exact algorithms for extracting conserved structured motifs from a
set of DNA sequences. Structured motifs may be described as an ordered collection of p≥ …

The recent explosion in available bacterial genome sequences has initiated the need to
improve an ability to annotate important sequence and structural elements in a fast, efficient …

Microarray analyses are providing a plethora of data concerning transcriptional responses to
specific gene regulators and their inducers but do not distinguish between direct and indirect …

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 …

Even though every cell in an organism contains the same genetic material, each cell does
not express the same cohort of genes. Therefore, one of the major problems facing genomic …

We have developed a set of methods and tools for automatic discovery of putative regulatory
signals in genome sequences. The analysis pipeline consists of gene expression data …

Entropy measures of DNA sequences estimate their randomness or, inversely, their
repeatability. L-block Shannon discrete entropy accounts for the empirical distribution of all …