I am a Professor of Applied Mathematics at the Massachusetts Institute of Technology (MIT), and head of the Computation and Biology group. I am also a member of the Theory of Computation group at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL). The Computation and Biology group, led by Professor Bonnie Berger, works on a number of problems at the interface of algorithms and biology. Many of the advances in modern biology revlove around recent advances in automated data collection and the subsequent large data sets drawn from them. We design algorithms to gain biological insights from this data and from future sources. We work on a diverse set of problems, including Protein Folding, Network Inference, Genomics, and Disease Classification. Additionally, we collaborate closely with biologists implementing these new techniques in order to design experiments to maximally leverage the power of computation for biological explorations.

Our work on protein structure prediction has led to a number of programs for predicting protein folds from primary sequence data, discovering novel sequence-structure motifs, generating near-native decoys, side-chain packing, and threading. Our work in mathematical models of virus shell assembly introduced a local-rules model for explaining the self assembly of viral shells. Our work in genomics has focused primarily on annotating genes, regulatory motifs, and conserved secondary structures through interspecies comparison. Our work in systems biology has resulted in a program that determines the optimal sampling strategy for time-series expression experiments. All of our programs are freely available for academic use.

The group has continued its efforts in protein structure prediction by updating our coiled-coil programs (i.e., Paircoil2, Multicoil2) and ß-structure prediction and modeling programs (BetaWrapPro), in collaboration with the Keating and King labs (MIT Biology) respectively. BetaWrapPro has recently been awarded a Best Structure Poster award at RECOMB 2005. Our work on beta-helices has provided good computational models for prions and amyloids, which are being tested by the Lindquist (Whitehead and MIT) and Gusella (Harvard Med) labs. We are currently applying our expertise in structure prediction and comparative genomics to functional analysis of protein active sites and binding sites. A recent collaboration with the Perrimon lab (Harvard Med) involves the use of RNA interference (RNAi) for the purpose of elucidating protein-protein interaction networks and signalling pathways. We are also exploring the use of structure to enhance the network-centric perspective of biological systems.

See our list of highlighted publications for our current research papers. In addition, be sure to check the home pages of group alumni who continue to make exciting contributions in many areas of science.

The seminar series focuses on highlighting areas of research in the field of Computational Molecular Biology. This is the seminar's fourth year. Professor Berger co-hosts the series with Professor Peter Clote of Boston College's Biology and Computer Science Departments. The seminar is co-sponsored by the Department of Mathematics at the Massachusetts Institute of Technology (MIT), and the Theory of Computation group at the MIT's Computer Science and Artificial Intelligence Laboratory (CSAIL). Information concerning the series can be found at the seminar's web page http://www-math.mit.edu/compbiosem/.

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