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 am a member of the Manchester Centre for Integrative Systems Biology, and of the Machine Learning and Optimization research group. My active areas of research are:

  • Development of modelling 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.
  • Construction of biochemical models: I am currently working on models of mammalian iron metabolism, eukaryotic translation, and microbial central metabolism. I am also developing methods for the construction of large-scale kinetic models of entire cells.
  • 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).
  • Biological data mining using machine learning: to analyse the large amounts of data produced in systems biology experiments, such as looking for common or unusual patterns in those data, or to classify (and identify the determinants) predefined behaviours.

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 am mentor projects under an NSF Research Education for Undergraduates project on Modeling and Simulation in Systems Biology that takes place every Summer. Interested students should apply through this page.

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YouTube channel

geeky blog