Informatics Challenges for Pharmacogenetics
Pharmacogenomics is the study of how human genetic variation impacts drug response phenotypes. We are building the PharmGKB (http://www.pharmgkb.org/) to catalog all knowledge of gene-drug relationships to support discovery and application of pharmacogenomics. From this effort arise important informatics challenges. I will discuss our work in text mining to extract relationships between drugs and gene variants, our use of this information to create tools for predicting gene-drug interactions, and our efforts building tools to assist in genetic association studies particularly focusing on drug response.
Russ Biagio Altman is professor of bioengineering, genetics, & medicine (and of computer science, by courtesy) and chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing technology to basic molecular biological problems of relevance to medicine. He particularly interested in informatics methods for advancing pharmacogenomics, the study of how human genetic variation impacts drug response (e.g. http://www.pharmgkb.org/). Other work focuses on the analysis of functional sites within macromolecules and the application of algorithms for determining the structure, dynamics and function of biological macromolecules (http://features.stanford.edu/). Dr. Altman holds an M.D. from Stanford Medical School, a Ph.D. in Medical Information Sciences from Stanford, and an A.B. from Harvard College. He has been the recipient of the U.S. Presidential Early Career Award for Scientists and Engineers and a National Science Foundation CAREER Award. He is a fellow of the American College of Physicians, the American College of Medical Informatics, and the American Institute of Medical and Biological Engineering. He is a past-president and founding board member of the International Society for Computational Biology, and an organizer of the annual Pacific Symposium on Biocomputing. He leads one of seven NIH-supported National Centers for Biomedical Computation, focusing on physics-based simulation of biological structures (http://simbios.stanford.edu/) . He won the Stanford Medical School graduate teaching award in 2000. He is a member of the Institute of Medicine of the National Academies.