My research develops computer science techniques for large-scale comparative genomics and hierarchical modeling of biological systems to better understand the mechanisms of eukaryote genome evolution and the ways that genes and proteins cooperate to realize cellular functions. In my research team we develop tools and algorithms for comparative genomics of eukaryotic microorganisms, inference of interaction and metabolic networks, and construction of hierarchical stochastic models of cell behavior, using techniques from data-mining, modeling, combinatorial analysis and formal methods.