© 2000 - 2014 Virginia Bioinformatics Institute
Sunday, 20 April 2014
, , PhD
Faculty - ,

Adjunct Faculty, Virginia Bioinformatics Institute
Adjunct Associate Professor, Department of Biochemistry, Virginia Tech


Biochemical Networks Modeling Group | Publications | COPASI: biochemical network simulator


  • Administrative Assistant: Jodi Lewis
    Phone: (540) 231-0714
    Email: jlewis@vbi.vt.edu

Professional Preparation

  • University of Wales, Aberystwyth, United Kingdom, Biochemistry, PhD, 1994
  • Post-doctoral fellowship, Computational Biology, University of Wales, Aberystwyth, United Kingdom, 1994-97
  • Program Leader for Pathways, National Center for Genome Resources, Santa Fe, NM, 1999-2000

Research Interests

  • Modeling and simulation of biochemical systems
  • Global optimization and inverse problems
  • Management and analysis of systems biology data sets
  • Oxidative stress and its cellular regulation
  • Reverse-engineering of biochemical networks


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.

Selected Publications

de la Fuente A, Brazhnik P, Mendes P. Linking the genes: inferring quantitative gene networks from microarray data. Trends in Genetics. 2002;18:395–398.

Moles CG, Mendes P, Banga JR. Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Research. 2003;13:2467–2474.

Martins AM, Camacho D, Shuman J, Sha W, Mendes P, Shulaev V. A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures. Current Genomics. 2004;5:649–663.

Camacho D, de la Fuente A, Mendes P. The origin of correlations in metabolomics data. Metabolomics. 2005;1:53–63.