Research Interests

[Back to Doug] [Address] [Academics] [Honors] [Invited Presentations] [Public Service] [Publications] [Recent Presentations] [Research] [Research Abstract] [Teaching]

I retired from research in May 2008 in order to dedicate my time to teaching full time. My research group's primary objective was to understand the flow of genetic information from the genome to the phenotype of an organism. This included understanding the sequence-structure dependencies and the structure-function dependencies of macromolecules. These goals represent the bioinformatic and functional-genomic approach to predicting structure and function from sequence. Specifically, we developed computer representations that could discover structural and functional properties of DNA, RNA and protein from sequences and from first principles. We spent much of our time learning the first principles of molecular and structural biology from known examples. We were also interested in predicting the interactions between ligands and proteins and between two interacting proteins.

The problems described above are also fundamental to understanding molecular biology and medicine. Functional genomics leads to novel diagnostic methods for both inherited and infectious disease. Analyses of protein structure and interactions results in discovery of new drug targets and rational drug design

We attacked these critical problems using a variety of different representations of sequences, structures and functions. Multiple representations of sequences include simple consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches as well as computer simulations. Much of our work consisted of developing a new representation of a structure or a function of a macromolecule, applying the methods of machine learning to this representation, and then evaluating the accuracy of the method. We have developed novel representations of sequence correlations that have predicted amino acid side chain interactions that stabilize protein strands and helices. We developed novel algorithms for aligning sequences that give insight into the secondary structure of proteins. We developed novel methods for discovering both sequence and structural motifs in proteins that help establish semantics of protein structure and function. All of the results of our research efforts are available from our Web page: http://brutlag.stanford.edu/ . Our publications are also available in both abstract and in full text format at http://cmgm.stanford.edu/~brutlag/Publications.html

[Back to Doug] [Address] [Academics] [Honors] [Invited Presentations] [Public Service] [Publications] [Recent Presentations] [Research] [Research Abstract] [Teaching]