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 …

Regulation of gene expression is central to many biological processes. Although
reconstruction of regulatory circuits from genomic data alone is therefore desirable, this …

Identifying master regulators of biological processes and map** their downstream gene
networks are key challenges in systems biology. We developed a computational method …

The response of Arabidopsis thaliana to low-oxygen stress (hypoxia), such as during shoot
submergence or root waterlogging, includes increasing the levels of∼ 50 hypoxia …

Comprehensive identification of all functional elements encoded in the human genome is a
fundamental need in biomedical research. Here, we present a comparative analysis of the …

The prediction of regulatory elements is a problem where computational methods offer great
hope. Over the past few years, numerous tools have become available for this task. The …

Background The regulatory map of a genome consists of the binding sites for proteins that
determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was …

Transcription patterns shift dramatically as cells transit from one phase of the cell cycle to
another. To better define this transcriptional circuitry, we collected new microarray data …

Biological networks are the representation of multiple interactions within a cell, a global view
intended to help understand how relationships between molecules dictate cellular behavior …

A central problem in the bioinformatics of gene regulation is to find the binding sites for
regulatory proteins. One of the most promising approaches toward identifying these short …