2004-2005 DISTINGUISHED LECTURERS Computer Science and Engineering JEFF THORNE Statistical Genetics and Bioinformatics North Carolina State University November 12, 2004 KIM BOYER Department of Electrical Engineering The Ohio State University November 19, 2004 DAN REED Institute for Renaissance Computing UNC-Chapel Hill, Duke & NC State December 3, 2004 JACK DONGARRA Department of Computer Science The University of Tennessee - Knoxville February 4, 2005 KANG G. SHIN Electrical Engineering and Computer Science The University of Michigan February 18, 2005 For details see http://www.cse.sc.edu/~mgv/colloquia/index.html Distinguished Lecture Series November 12, 2004 University of South Carolina Columbia, South Carolina ABSTRACT “Combining Protein Evolution and Protein Structure” PROFESSOR JEFFREY L. THORNE Jeff Thorne was raised in Kohler, Wisconsin. In 1986, he earned B.S. degrees in mathematics and molecular biology from the University of Wisconsin – Madison. In 1991, he received a Ph.D. in Genetics from the University of Washington. His thesis advisor was Dr. Joseph Felsenstein and his dissertation topic was statistical aspects of DNA and protein sequence alignment. Jeff was a postdoctoral associate with Dr. Gary Churchill in the Biometrics Unit at Cornell University. He joined the North Carolina State University faculty in 1993. He holds a joint appointment in the Genetics and Statistics Departments and is actively involved in the Bioinformatics Graduate Program. Thorne’s research focus is the development of statistical techniques for studying molecular evolution. He currently has two main lines of research. One concerns the relationship between protein structure and protein evolution. The other involves estimating chronological rates of molecular evolution as well as speciation times by combining fossil information with DNA or protein sequence data. by Jeff Thorne North Carolina State University Friday, November 12 2004 Amoco Hall Swearingen Engineering Complex (SWGN 1C01) 2:30 pm Jeff and his wife Leigh are the proud parents of a baby girl named Evelyn and an Australian Shepherd named Sterling. Refreshments immediately following in the lobby area outside Amoco Hall. The relationship between phenotype and survival of the genotype is central to both genetics and evolution. Protein-coding DNA sequences are genotype whereas protein tertiary structures are a fundamental unit of phenotype. We are studying the impact of protein structure on the evolution of protein-coding DNA sequences. In contrast to widely used procedures that largely model change of genotype as being independent of phenotype, our approach incorporates phenotype via adoption of sequence-structure compatibility measures that computational biologists originally designed for the purpose of protein fold recognition. A consequence of our genotype-phenotype models is the necessity to abandon computational strategies that are conventionally employed to study molecular evolution. In addition to protein structure, there are diverse other aspects of phenotype that are being predicted in silico by computational biologists. We emphasize that these other in silico systems can also be exploited to better characterize the evolutionary relationship between genotype and phenotype.