[bioinfo] CS 591 BIO: REMINDER: Talk TODAY by Prof. Zoi Rapti (Math, UIUC)

[Sinha, Saurabh]

Hello,
   our speaker today is Prof. Zoi Rapti of the Mathematics department
(UIUC), who will be presenting her work on DNA instability. Details of the
talk appear below.

   DATE: Friday, April 10
   TIME: 1100 AM - 1200 noon
   PLACE: 4403 Siebel Center.

   thanks,
   Saurabh

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Title: Thermodynamic Signatures of Human Promoter Sequences

Abstract: Using an Ising-type model for the DNA double strand, we analyzed
the thermodynamic instability profiles of human promoter sequences. The
sequences were classified as containing the following core promoter
elements and\or combinations of them: TATA-box, DPE, BRE, Inr, and GC-box.
The analysis was based on the opening probability profiles, that are
obtained by calculating probabilities of having k (k=1-7) consecutive
base-pairs
open starting at site n versus n. We report results that associate the
location of peaks in the probability instability profiles with the
presence of core promoter elements at these locations and in some cases
with the location of transcription start sites. We also compare the
average thermodynamic profiles of core promoter sequences to random and
shuffled sequences and extract characteristic trends. This is joint work
with Ruth Kantorovitz, Vlado Gelev, and Anny Usheva.

Brief Bio: Z. Rapti received her Ph.D. in Mathematics at the University of
Massachusetts, Amherst in 2004. She spent one year at the Institute for
Advanced Study in Princeton and then moved to UIUC in 2005 as a J.L.Doob
Research Assistant Professor. Since 2008 she is an Assistant Professor in
the Department of Mathematics. Her principal research interests lie in
Differential Equations (stability of solutions to nonlinear evolution
equations) and Mathematical Biology (DNA modeling and denaturation).