Research Projects

We work on a number of diverse research projects, most of which are collaborations with other groups (at VBI and elsewhere). We are funded by a variety of sources though they do not necessarily map 1-to-1 with the projects.

Software for simulation of biochemical networks

This started over a decade ago with Pedro Mendes' Gepasi simulator. Gepasi is widely used as a research tool in many labs. Currently the group is working in collaboration with Ursula Kummer's group at the European Media Lab (Heidelberg) to develop a new simulator COPASI. This has many new features and will become our main biochemical simulator when it will be released. COPASI will be free for non-profit research use. Also under this section, we carry out research in numerical optimization methods applied to biochemical networks modeling, with collaboration by Julio Banga's group in the Marine Research Institute (Vigo, Spain).

Gene networks

Our involvement in gene networks started with an interest in including gene regulation in metabolic models. Since then we developed methods for reverse-engineering gene networks from gene expression data (eg microarray), and have created a system for generating artificial gene networks of arbitrary size and complexity. Read more...

Bioinformatics for integrated functional genomics

We believe that the most powerful way of observing the behavior of cells is, currently, to monitor their gene expression, protein and metabolite levels simultaneously. However such integrated data sets require appropriate databases and advanced and diverse analysis methods. We are involved in three federally funded projects of this kind:

• biotic and abiotic stress in the model legume Medicago truncatula, a project in collaboration with colleagues at the Samuel Roberts Noble Foundation and Southeastern Oklahoma State University. This is funded by the NSF Plant Genome Research Program.
• effects of oxidative stress on the yeast Saccharomices cerevisiae, a project in collaboration with the Laubenbacher and Shulaev groups at VBI. This is funded by the National Institute of General Medical Sciences.
• Effects of drought and cold stress on the grape Vitis vinifera and on wine quality, a project led by collaborators at the University of Nevada-Reno and funded by the NSF Plant Genome Research Program.

Bioinformatics for metabolomics

Metabolomics is becoming increasingly important in functional genomics, systems biology or just plain biochemical research. However there is a big need of informatic tools to store and analyze such data. We are working towards meeting this demand by:

• constructing databases for metabolomics data
• developing methods for analysis of metabolite concentration profiles
• developing methods for processing raw chromatographic, electrophoretic and mass spectral data.
• working with the community to define metabolomics data standards.

We collaborate with the Shulaev group (VBI), Sumner group (Noble Foundation), Cramer group (Univ. Nevada-Reno), and Smith group (Southeastern Oklahoma State Univ.)

Ascorbic acid biosynthesis in Arabidopsis thaliana

We collaborate with Craig Nessler and Boris Chevone in Virginia Tech's Plant Pathology and Physiology Department on metabolic engineering of vitamin C synthesis in plants. More information on this project here...

Malaria bioinformatics

The group is constructing a database system to organize all the current knowledge on the biochemistry and genetics of the malaria parasite Plasmodium falciparum. This effort consists in collecting the relevant facts from the literature and storing them on our B-Net database. This work is carried out in collaboration with David Sullivan at the Johns Hopkins Bloomberg School of Public Health, under the umbrella of a collaboratory between that institution and VBI. More information on this project here...