Pedro Mendes

My research is in the area of computational systems biology, which aims to better understand biological systems through the use of computer models. My active areas of research are:

- Development of modeling and simulation software, particularly the popular simulator COPASI. I have also been actively involved in the development of standards for systems biology, such as the systems biology markup language (SBML).
- Construction of biochemical models: I am currently working on models of mammalian iron metabolism, eukaryotic translation, and microbial biofilms.
- 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.

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.