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Dr. Mendes’ research at VBI is centered broadly around computer simulation and analysis of biochemical networks. This is comprised of three components: development of simulation software (Gepasi and now COPASI), modeling of gene expression in the context of metabolic networks, and bioinformatic support for metabolomics.
Dr. Mendes is the author of the popular biochemical simulation software Gepasi. This allows biochemists to model biochemical networks without having to write the mathematics explicitly (the program does that internally). Gepasi is thus targeted at those biochemists that need to do simulation but cannot spend time programming. More recently Dr. Mendes is engaged in collaboration with Dr. Ursula Kummer of EML Research, which has resulted in a new simulator called COPASI, which is the natural successor to Gepasi.
Research in Dr. Mendes’ group is active in the area of modeling gene networks together with biochemical pathways. The philosophy is that gene signaling, and metabolic networks are tightly interconnected such that it makes sense to model the two together. In order to construct these integrated networks that include gene expression and metabolism, it is necessary to carry out experiments that include comprehensive measurements of biomolecules at the genome level (RNA, proteins, and metabolites). Such data are generated in collaboration with Dr. Vladimir Shulaev of VBI, as well as with colleagues at the Samuel Roberts Noble Foundation (Ardmore, OK), and the University of Nevada-Reno.
For more information visit Dr. Mendes’s Research Group Page (Biochemical Networks Modeling Group).
Other interests are in management of data from genomics, proteomics and metabolomics, for which his research group has constructed the DOME system. Dr. Mendes is also very active in the reverse-engineering of biochemical networks.
Dr. Mendes serves in the “Modeling and Analysis of Biological Systems (MABS)” study section of the National Institutes of Health, and has been a member of several scientific committees and advisory boards.
Benchmarking parameter estimation and reverse engineering strategies
as author at Workshop on Parameter Estimation in Systems Biology, Manchester 2007,