People:
Under Construction!
Richard Bonneau, PI
Kevin Drew, Research Assistant
I am a research assistant in the Bonneau Lab currently working on the HPF and HPF2 projects. I also work on the BioNetBuilder project. My research interests include protein function prediction through structral analysis and grid computing. I received my BS in Computer Science from the University of Iowa and my MS in Computer Science from the University of Chicago.
Glen Butterfoss, Postdoc
Thadeous Kacmarczyk, Grad Student
I am a biology graduate candidate trying to learn biology, mathematics, statistics, physics, chemistry, and computer science. My research is resolving how to integrate various datasets into a biclustering method to elucidate genetic regulatory networks first for individual organisms (e.g. B. subtilis, E.coli) and then for multiple species across different clades. I enjoy in-line skating, wine, gummy bears, the caribbean, martial arts, my wife Catharine and son Sorin, dungeons and dragons, animals and sunshine.
Aviv Madar, Grad Student
I am a biology graduate student and my research focuses on inferring biological regulatory networks. Organisms must continually adapt to changing cellular and environmental factors (e.g. oxygen levels) by altering their gene expression patterns. At the same time, all organisms must have stable gene expression patterns that are robust to small fluctuations in environmental factors and genetic variation. Learning and characterizing the structure and dynamics of Regulatory Networks (RNs), on a whole-genome scale, is a key problem in systems biology. We are currently developing a Markov-Chain-Monte-Carlo (MCMC) optimization algorithm, which learns models that agree with the uncoupled as well as coupled dynamics of the system, and is constrained by the sparsity expected from biological systems. This should allow us to model the dynamics of a cell's mRNA expression levels, over longer time scale, such as the cell cycle.
Peter Waltman, Grad Student
