Older Projects

This is a list of research projects that we have undertaken in the past that are no longer active. We also provide here resources that were produced in these projects and are freely available, but which are no longer supported.

Metabolic Reconstructions

This was a collaboration with many groups around the world. A basic step in understanding cellular biology is to know all of its components and how they interact. A metabolic reconstruction is a network of molecules, reactions and genes involved in cellular metabolism. We have been involved in several metabolic reconstructions, but particularly for yeast and human (Recon2).

Mathematical modeling of yeast oxidative stress

This was a collaboration with R. Laubenbacher and V. Shulaev at the Virginia Bioinformatics Institute funded by the NIGMS and NSF. We conducted a systems biology study of the dynamics of the response of yeast to cumene hydroperoxyde through microrarrays, proteomics and metabolomics.

Metabolic Engineering of Plant Vitamin C Biosynthesis

This was a collaborative project with Craig Nessler, Argelia Lorence, and Boris Chevone at Virginia Tech funded by NSF and USDA. We discovered new myo-inositol oxigenase enzymes in Arabidopsis. Overexpressing these genes leads to plants with larger biomass (particularly roots).

Medicago truncatula functional genomics and bioinformatics

This was a collaboration with Rick Dixon of the S.R. Noble Foundation and was funded by the National Science Foundation. More details about this project on its NSF Plant Genome Research Program.

Grape Bioinformatics

This was a collaborative project led by Grant Cramer from the University of Nevada-Reno, and funded by the NSF Plant Genome Research Program. More information at the project's main website.


The DOME database system was constructed to support the data obtained from the Medicago, grape and yeast projects above. This system is no longer being developed, however we are happy to distribute the software to anyone who wants to use it. Unfortunately there are no means for us to provide support.