The Brutlag Bioinformatics Group is located in the Biochemistry Department at Stanford University and is also affiliated with the Stanford Center for Biomedical Informatics Research in the Department of Medicine, Stanford Medical School. The primary goal of our group was understanding the meaning of the genomic information and how this information is expressed using computational means. We were interested in the problems of predicting biological function of genes and gene products from their sequence and structure (sometimes known as functional genomics). We were also interested in understanding how and when genes are expressed. We developed advanced profile and sequence motifs for representing structural and functional aspects of proteins (EMOTIF, EMATRIX, 3MOTIF and 3MATRIX). These methods can be used for assigning functions to unidentified protein sequences.

We 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 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 currently involved in teaching Computational Molecular Biology. The following courss is available both at Stanford and online via the Stanford Center for Professional Development.

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

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