Numerous studies have demonstrated the importance of altered gene expression in disease pathophysiology. Thus, modification of gene expression has emerged as an important therapeutic strategy.1 Agents that inhibit the transcription of disease-mediating genes or transactivate the expression of genes whose products disrupt pathophysiological processes are being developed. Regulation of gene expre...

In this issue of Cell, Hallikas et al. (2006) and Wei et al. (2006) describe different ways of identifying direct targets of transcription factors and their corresponding regulatory sequences in the genome. Although still under development, these studies provide an efficient way to decipher regulatory networks.

Transcriptional regulation is mediated by a battery of transcription factor (TF) proteins, that form complexes involving protein-protein and protein-DNA interactions. Individual TFs bind to their cognate cis-elements or transcription factor-binding sites (TFBS). TFBS are organized on the DNA proximal to the gene in groups confined to a few hundred base pair regions. These groups are referred to...

A transcription factor that regulates skeleton formation in sea urchin embryos has evolved a new domain that is essential for this process.

Motivation: Generating small models for which there may exist very little training data presents a crucial problem in computational biology, namely the trade-oo between model speciicity and under-tting the data. There are a bevy of superior modeling techniques; however, certain domain speciic problems, such as modeling the regulatory regions in intergenic DNA impose constraints on the modeling ...