Background The detection of conserved motifs in promoters of orthologous genes
(phylogenetic footprints) has become a common strategy to predict cis-acting regulatory …

Heat-shock genes have a well-studied control mechanism for their expression that is
mediated through cis-regulatory motifs known as heat-shock elements (HSEs). The …

Much of biological diversity is thought to arise from changes in regulatory networks.
Although the role of transcriptional regulation has been well established, the contribution to …

Convergent evolutionary events in independent lineages provide an opportunity to
understand why evolution favors certain outcomes over others. We studied such a case …

The related yeasts Saccharomyces cerevisiae and Candida albicans have similar genomes
but very different lifestyles. These fungi have modified transcriptional and post-translational …

Protein interaction networks are an important part of the post-genomic effort to integrate a
part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes …

The fundamental mechanisms that control eukaryotic development include extensive
regulation at the level of transcription. Gene regulatory networks, composed of transcription …

Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More
difficult, however, is experimental testing of the inferences about gene function that can be …

Comparative analysis is a fundamental tool in biology. Conservation among species greatly
assists the detection and characterization of functional elements, whereas inter-species …

Co-evolution of transcriptional regulatory proteins and their sites of action has been often
hypothesized but rarely demonstrated. Here we provide experimental evidence of such co …