Speaker: Dr Gary Stormo, Professor, Washington University Department of Genetics
Host: Michael Zhang

Title: Modeling protein-DNA interactions: experimental and computational approaches

Time: Aug 1, 10:00 ~ 11:30
Place: FIT 1-312

Abstract:
Protein-DNA interactions are an essential part of the regulation of gene expression. New experimental methods have greatly increased the amount of data available that can be used to develop quantitative models for the specificity of transcription factors. This talk will described new computational approaches that take advantage of the new experimental technologies to provide improved models of specificity and aid in the design of proteins with novel specificity.

Research Interests:
Molecular Biology: Most of the experimental work is focused on understanding the regulation of gene expression, and especially the basis of specificity in protein-nucleic acid interactions. We analyzed how the affinity of certain proteins for DNA changes depending on the sequence of the DNA, and conversely for changes in the key residues of the protein. We’ve developed methods that allow us to obtain accurate, quantitative data in large amounts, which can be used to develop models for the interactions.
Computational Biology: Much of the computational work is also involved with modeling protein-nucleic acid interactions, and relies on a close collaboration with the experimental work. In addition, we have been developing new methods for RNA structure prediction using graph theory approaches. We are also working on methods for predicting the function of DNA domains, such as promoters, exons, introns, and others. A recent interest is in using expression array data to help in modeling genetic regulatory networks.