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.