Prokaryotic Gene Regulation Center for Bioinformatics Wadsworth Center

The transcription regulatory network is arguably the foundation of cellular function, since it exerts the most fundamental control over the abundance of virtually all of a cell's macromolecules. Comparative genomics has proven to be a powerful bioinformatics method with which to study transcription regulation. We believe that an understanding of microbial gene regulation is key to understanding how microbes: cause disease, remediate toxic chemicals, reduce heavy metals, and contribute to the biosphere. Our efforts are aimed toward identifying a cell's complete transcription regulatory network and underlying molecular mechanisms through the application of rigorous bioinformatic and statistical tools (e.g., Gibbs sampling).

Escherichia coli - our model system	Citation
Transcription Factor Binding Sites have been predicted genome-wide and their statistical significance has been evaluated. The results of those predictions are available as a searchable database.	McCue et al., 2002 McCue et al., 2001
Regulons were predicted by clustering the putative regulatory motifs described above using a Bayesian motif clusterer. These data were also used in the development of an application for identifying cis-trans regulatory connections.	Tan et al., 2005 Qin et al., 2003

Rhodopseudomonas palustris - a study in metabolic flexibility	Citation
A comparative genomic study of R. palustris has been completed and Phylogenetic Footprinting and Clustering data are available.	Conlan et al., 2005

Microbial species comparison	Citation
Software has been developed for the comparison of microbial species using the distribution of pairwise percent identities between homologous sequences. [download page]	Conlan et al., 2006