Anne Condon
University of British Columbia

Computational Challenges and Opportunities in RNA Secondary Structure Prediction
Abstract: 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, progress in solving these problems, and directions for future research. No prior biological background will be assumed for the talk.

Biography: Anne Condon is a Professor of Computer Science at the University of British Columbia and Associate Dean in the Faculty of Science. Much of her current research focuses on computational prediction of nucleic acid structure, with applications to design of novel structures and gene synthesis. Her research contributions span computational complexity theory, hardware verification, biomolecular computation, and combinatorial auctions.

She has received an ACM Distinguished Dissertation Award, NSF National Young Investigator Award, and University College Cork Distinguished Alumna Award for her work, and currently holds the NSERC/GM Canada Chair. Anne received her BSc degree (1982) from University College Cork, Ireland and PhD (1987) from the University of Washington. Prior to her position at UBC, she was a faculty member at University of Wisconsin from 1987–1999.

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