Title: "From Nucleotide Sequences to Secondary Structures, and Back Again"
Speaker: Dr. Christine Heitsch, Department of Mathematics, University of Wisconsin -Madison
Place: SMITH 108; Tuesday, April 20, 2004; 4:30pm


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.

(This is a candidate for the Bioinformatics COALESCE hires in the School of Science. To meet with the candidate, please contact RW Doerge at doerge@purdue.edu)

See http://www.stat.purdue.edu/~doerge/BIOINFORM.D/SPRING04/sem.html for a full scheule of BIOINFORMATICS SEMINARS.