Pedro Mendes, PhD
Professor at the Center for Cell Analysis and Modeling and Center for Quantitative Medicine and the Department of Cell Biology at the University of Connecticut Health Center, .
Education
Licenciado (BSc) in Biochemistry, by the University of Lisbon (1983-1988)
PhD by the University of Wales Aberystwyth (1990-1994), thesis titled Computer simulation of the dynamics of biochemical pathways), Supervisor: Douglas B. Kell
Publications
Research Interests
My research is in the area of computational systems biology, which aims to better understand biological systems through the use of computer models. I have active projects in the following areas of research:
- Development of modeling and simulation software: I was the author of the popular simulator Gepasi and now the leader of the new COPASI simulator (w/ U. Kummer). I have also been actively involved in the development of SBML, the systems biology markup language, and the MIRIAM proposal for model annotation.
- Modeling mammalian iron physiology at different scales. This includes models of specific cell types, whole-body models, and models of tissues.
- Parameter estimation and systems identification: I have pioneered the application of numerical global optimization in biochemical kinetic modelling. I am interested in using formal systems identification techniques in systems biology, particularly for reverse engineering models from data.
- Reverse engineering biological networks: a long-term objective of systems biology is to be able to construct models directly from large-scale genomics, proteomics and metabolomics data sets. I have been interested in this problem for a while, having been involved in the development of a few methods for reverse engineering, as well as creating artificial networks to benchmark that type of algorithms (eg the AGN system).
- In the past I developed models for microbial central metabolism, eukaryotic protein translation, and mixed-species biofilms.
Research in the areas listed above requires a broad interdisciplinary approach and I work with people from most areas of science, either in my own research group or as collaborators.
PhD Students
I have supervised more than 15 PhD students. (See the full list here)
Undergraduate students
I mentor summer projects for UConn Storrs students under the Health Research Program program. I can also mentor summer projects for undergraduate students of other Connecticut colleges under the Partnership for Innovation and Education program.
