With the availability of fully sequenced genomes and the development of high-throughput functional genomics technologies, we now have the tools to look at the molecular biology of an organism from a systemic viewpoint. Systems biology is a dynamic and highly interdisciplinary field, requiring input from biology as well as engineering, physics and mathematics. One of our main interests is the development of methods to analyze functional genomics data and integrate them in models that reflect the regulatory wiring and modularity of biological systems, and ultimately predict their behavior. We are also developing user-friendly computational tools to assist wet-lab researchers in the interpretation of large-scale datasets and biological networks.

Evolution of Biological Systems

 

We are especially interested in figuring out how biological systems evolve. One particular aspect that we study intensively, in collaboration with the Van de Peer lab, is how gene and genome duplications affect the evolution of organisms. Expansion of gene families by duplication and subsequent functional diversification is considered of major importance for the development of biological novelties during evolution. However, we have only begun to elucidate the mechanisms underlying evolutionary innovation through gene duplication. Recent studies have shown that regulatory gene duplicates (transcription factors, signal transducers and developmental genes) have been retained in excess after genome duplications in A. thaliana and other organisms. More importantly, it seems that duplicates in many regulatory gene families are retained almost exclusively after genome duplication, suggesting a key role for large-scale gene duplication events in plant evolution. In addition, we foun!

 d indications that genome duplications are mainly evolutionary successful under certain circumstances, e.g. after mass extinction events, raising the intriguing possibility that ecological catastrophes may ultimately lead to more complex plants.