Pedro Mendes, PhD


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


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.

@gepasi twitter feed

pedrik Flickr stream

YouTube channel

geeky blog