Chair: Sanjoy Dasgupta
Systems biology has grown rapidly in over past few years and is believed by many to be a transforming development in the life sciences. This field has grown mainly around four areas of emphasis: 1) generation of high-throughput data for organisms and diseases of interest, 2) reconstruction of the biochemical reaction and interaction networks that underlie cellular functions, 3) the development of mathematical methods to characterize the functional states (i.e., physiological states of networks) and 4) the use of computer-aided design in biological experimentation. Activities in these four areas will be discussed.
Bernhard Palsson is a Professor of Bioengineering and Adjunct Professor Medicine at the University of California, San Diego where his research focuses on 1) reconstruction of genome-scale biochemical reaction networks, 2) development of mathematical analysis procedures for genome-scale models, and 3) experimental verification of genome-scale models. Prof. Palsson holds a Ph.D. from the University of Wisconsin (1984) and prior to joining UCSD held a faculty position at the University of Michigan (1984-1995). Prof. Palsson is the author of over 200 peer reviewed scientific articles, and of the recently published book "Systems Biology: Properties of Reconstructed Networks", he also holds over 20 U.S. biotechnology patents. Prof. Palsson is the recipient of several fellowship awards, is a member of the editorial boards of several bioengineering and biotechnology journals, and has co-founded several biotechnology companies, including Aastrom Biosciences, Cyntellect, and Genomatica.
In the last decade computer scientists have found new computational challenges in molecular biology. I discuss recent advances and present some open combinatorial problems in different areas of computational molecular biology such as genome rearrangements, regulatory motif finding, and molecular evolution.
Pavel Pevzner holds the Ronald R. Taylor Chair in Computer Science. He joined the UCSD faculty in 2000, following five years in the University of Southern California's Department of Mathematics. From 1992-95, he was an associate professor at Pennsylvania State University. From 1990-92 Pevzner was a postdoctoral researcher at USC. He received his Ph.D in 1988 from the Moscow Institute of Physics and Technology. Pevzner is the author of the book "Computational Molecular Biology: An Algorithmic Approach" (MIT Press, 2000) and also "Introduction to Bioinformatics Algorithms", co-authored with Neil Jones (MIT Press, 2004). He is an executive editor of the "Journal of Computational Biology," and co-founder of the International Conference on Research in Computational Biology (RECOMB).
The Human Genome Project, the International HapMap Project, the Cancer Genome Project, and related Human DNA sequence initiatives, have raised a number of questions about Human genetic diversity. These questions range from human population origins and migration patterns, admixture among humans from different geographic locations, the exploitation of genomic diversity in gene discovery (i.e., mapping) approaches, and the accommodation of this diversity in medical and public health practices. In this talk, descriptions of the motivations and resources associated with these very large-scale initiatives will be provided. In addition, the talk will focus on an overview and description of the open questions in the field of modern applied human population genetics that invite mathematical and statistical challenges.
Nicholas Schork is currently a Professor in the Departments of Biostatistics and Psychiatry at the University of California at San Diego. He is also an SDSC fellow, a Project Leader for Cal-IT2, Co-Driector of the Center for Human Genetics and Genomics, and Director of Bioinformatics at the Cancer Center. Prior to his appointment at UCSD, Dr. Schork was an Associate Professor of Epidemiology and Biostatistics at Case Western Reserve University in Cleveland, Ohio and an Associate Professor of Biostatistics at Harvard University. He was also formerly the Associate Director of the Program for Population Genetics at the Harvard School of Public Health, as well as an Adjunct Associate Staff Scientist at the Jackson Laboratory in Bar Harbor, Maine. Dr. Schork earned a B.A. in Philosophy, an M.A. in Philosophy, an M.A. in Statistics, and a Ph.D. in Epidemiology all from the University of Michigan in Ann Arbor, Michigan. Dr. Schork's research interests are varied, but primarily focus on the understanding the genetic basis of complex traits and diseases. Dr. Schork develops mathematical, statistical, and computational models and analytic tools that can be applied to genetic studies. In addition, much of his work considers how one can integrate information from different studies and study designs in order to draw inferences about the complexities that underlie disease and phenotypic expression.