Monday, November 13, 2006
11:00 AM
CSB 209
David Mathews
U. Rochester (Biochemistry & Biophysics)
RNA Secondary Structure Prediction: Methods and Applications
RNA is now known to perform many critical roles in cellular function. This talk will introduce the importance and organization of RNA structure. The secondary structure of RNA, the sum of the canonical (AU, GC, and GU) base pairs can be predicted on the basis of free energy minimization using a dynamic programming algorithm. Our group has written a dynamic programming algorithm that can find the lowest free energy structure common to two sequences. This algorithm, called Dynalign, is significantly more accurate at RNA secondary structure prediction. We have also shown that Dynalign-predicted folding free energies can be used to discover functional RNA sequences from complete genome sequences.

Bio: David Mathews graduated with a Physics BS degree from the University of Rochester in 1994. He was then accepted by the Medical Scientist Training Program (M.D.-Ph.D.) at the University of Rochester Medical School. In 2002, he received a Ph.D. in Chemistry for his study of RNA structure and stability in Douglas Turner's lab. In 2003, he received his MD. After a year's post-doctoral with David Case, studying RNA dynamics at The Scripps Research Institute, San Diego, he returned for a faculty position in the Department of Biochemistry & Biophysics in the Center for Pediatric Biomedical Research. Dr. Mathews' group concentrates on the Computational Biology of RNA.