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Computer Science @ Rochester
Friday, November 21, 2008
11:00 AM
Computer Studies Bldg. Room 209
Anne Condon
University of British Columbia
Computational challenges and opportunities in RNA secondary structure prediction and design
DNA and RNA molecules have proven to be very versatile materials. Structures formed by RNA molecules play important regulatory and catalytic roles in the cell, and show promise in therapeutics. Molecular engineers can now design and realize nano-scale structures and sensors, and even simple machines with moving parts, built from DNA. Function follows form in the molecular world, and so our ability to understand nucleic acid function in the cell, as well as to design novel structures, is enhanced by reliable means for structure prediction.

Computational work on RNA structure prediction has focused on secondary structure - the set of base pairs that form when the molecule folds on itself. Algorithms which predict RNA and DNA secondary structure from the base sequence typically rely on models of the physical (thermodynamic) aspects of molecular folding. In this talk, we will describe some algorithmic and inference problems that arise in DNA/RNA secondary structure prediction from the base sequence and progress in solving these problems. We will also describe ways in which such structures are being designed for novel functions, and new directions for research in modeling and analysis of such designs.

No prior biological background will be assumed for the talk.

Bio: Anne received her B.Sc. degree (1982) from University College Cork, Ireland and Ph.D. (1987) from U. Washington. She was a faculty member at U. Wisconsin from 1987-1999. She won an ACM Distinguished Dissertation Award, NSF National Young Investigator Award, and University College Cork Distinguished Alumna Award for her work. She holds an NSERC/GM Canada Chair.

Refreshments will be provided at 10:45