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.
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.