Date: Wednesday, May 19, 2004
Time: 11:30 AM
Room: NAC 8/206 (Csc. Dept. Conference Room)
Speaker: Dr. Christine Heitsch
In the absence of complementary strands, single-stranded nucleotide sequences may hybridize with themselves or each other. For the short oligonucleotides or "DNA code words" found in many biotechnological applications such hybridizations prevent the DNA segments from performing their desired functions. In contrast, the self-bonding or "secondary structure" of organic RNA molecules is an essential part of their overall structure and function. Our goal is understanding the biological information encoded by the selective base pair hybridization of single-stranded DNA and RNA molecules. Toward that end, we focus on developing algorithms for the design of RNA secondary structures and DNA code words based on discrete mathematical models. We give results on strings encoding plane trees, the importance of helical segment quality, and the biochemical properties of random de Bruijn sequences. We also discuss some of the broader biological implications of this work ! in a less abstract setting.
Dr. Christine Heitsch is a postdoctoral fellow at the University of Wisconsin -- Madison, funded by the National Library of Medicine training grant, "Computation and Informatics in Biology and Medicine." An interdisciplinary researcher, she is affiliated with both the UW Madison Department of Chemistry and the Mathematics Department. Previously, Dr. Heitsch had been a postdoc in the theory group of the Department of Computer Science at the University of British Columbia. She received her Ph.D. in Mathematics from the University of California at Berkeley, writing a dissertation under the direction of John Rhodes. Her current research interests focus on problems at the juncture of computational biology, theoretical computer science, and discrete mathematics.