research overview  |  gene circuits & systems  |  metabolic engineering  |  infectious disease  |  organisms  |  resources

We are developing and applying novel computational tools to map and model system-wide properties of gene regulatory networks in microbes.

This work includes:
- Algorithms for regulatory network and metabolic pathway mapping
- Affymetrix expression profiling and data analysis
- Genetic engineering of metabolic and regulatory pathways
- Realtime gene expression analysis in microfluidic devices and bulk culture

We are applying these tools in multiple areas. We are mapping the regulatory and metabolic networks of Shewanella oneidensis in collaboration with the Shewanella Federation, and analyzing the models for ways to increase current generation by this electrogenic microbe. We are also building network maps in Pseudomonas aeruginosa and E. coli in order to identify mechanisms of virulence and drug resistance. For application to drug discovery, we are developing algorithms to identify the mechanism of action of drug candidates using whole-genome RNA expression profiles.

E. coli gene regulatory map
This map illustrates 1079 transcriptional regulatory interactions discovered using the CLR algorithm developed by bioinformatics PhD students Jeremiah Faith and Boris Hayete. The algorithm was used to mine 445 Affymetrix gene expression profiles available in the M3D database.