The primary goal of our group is to understand the meaning of the genomic information and how this information is expressed using computational means. We are interested in the problems of predicting biological function of genes and gene products from their sequence and structure (sometimes known as functional genomics). We are interested in predicting structure of protein and DNA from sequence, and understanding how and when genes are expressed.

We have developed accurate and rapid methods for comparing protein structures and structural database search (LOCK2 and FoldMiner). We are also interested in the areas of secondary structure prediction, discovery of promoters and other DNA regulatory sequences, small molecule and protein docking, identifying drug targets, and drug design.

We have also developed rapid methods for discovering transcription factor binding sites in coregulated genes. Both BioProspector and MDScan can take upstream sequences from co-regulated genes and can find conserved DNA consensus sequences even if they are very short (8bps), poorly coonserved (50%), interrupted, and present in less than 50% of the sequences.

We are also involved in teaching Computational Molecular Biology, Bioinformatics, Genomic and Proteomic courses. The following courses are available both at Stanford and online via the Stanford Center for Professional Development.

Biochemistry 218 Computational Molecular Biology http://biochem218.stanford.edu/

Biochemisttry 228 Computational Genomic Biology http://biochem228.stanford.edu/

Biochemisrty 238 Computational Proteomic Biology http://biochem238.stanford.edu/

Biochemistry 248 Computational Systems Biology http://biochem248.stanford.edu/ (in development)

We are no longer accepting applications for graduate students or postdoctoral fellows.