Research

Research Laboratories

Gene Regulation We aim to develop computational methods for understanding the molecular mechanism of gene regulation. Specifically, we develop novel ways to discover cis-regulatory elements in genomic DNA. Since such elements are of low information content, we pursue multiple approaches: (1) better characterizing transcriptional start sites and alternative proximal promoters; (2) detecting cis-element clusters using probabilistic models; (3) identifying genes that are co-regulated and taking advantage of the enrichment of the same cis-elements in their promoters.
Protein Docking and DesignWe develop methods to compute binding affinities between protein molecules. Combining this ability with a Fast-Fourier-Transform based search algorithm, we develop algorithms for predicting protein-complex structures. We can also search in the sequence space and predict mutations that lead to improved binding. In the wet-lab component of ZLAB, we produce mutant proteins according to computational predictions and test their binding affinities. The ultimate goal is to establish in vitro evolution procedures to fine-tune computational predictions.