2005 APS March Meeting
Monday–Friday, March 21–25, 2005;
Los Angeles, CA
Session B7: Women at the Forefront of Biological Physics
11:15 AM–1:39 PM,
Monday, March 21, 2005
LACC
Room: 408B
Sponsoring
Units:
DBP CSWP
Chair: Aihua Xie, Oklahoma State University
Abstract ID: BAPS.2005.MAR.B7.1
Abstract: B7.00001 : Computational Genomics Using Graph Theory
11:15 AM–11:51 AM
Preview Abstract
Abstract
Author:
Tamar Schlick
(New York University)
With exciting new discoveries concerning RNA's regulatory cellular
roles in gene expression, structural and functional problems
associated with DNA's venerable cousin have come to the forefront.
RNA folding, for example, is analogous to the well-known protein
folding problem, and seeks to link RNA's primary sequence with
secondary
and tertiary structures. As a single-stranded polynucleotide,
RNA's secondary structures are defined by a network of
hydrogen bonds, which lead to a variety of stems, loops,
junctions, bulges,
and other motifs. Supersecondary pseudoknot structures can also
occur and, together, lead to RNA's complex tertiary
interactions stabilized by salt and solvent ions in the natural
cellular milieu. Besides folding, challenges in RNA research include
identifying locations and functions of RNA genes,
discovering RNA's structural repertoire (folding motifs),
designing novel RNAs, and developing new antiviral
and antibiotic compounds composed of, or targeting, RNAs.
In this talk, I will describe some of these new biological
findings concerning RNA and present an approach using graph theory
(network theory) to represent RNA secondary structures.
Because the RNA motif space using graphs is vastly smaller
than RNA's sequence space, many problems related to
analyzing and discovering new RNAs can be simplified
and studied systematically. Some preliminary applications
to designing novel RNAs will also be described.\newline\newline
Related Reading\newline
H. H. Gan, S. Pasquali, and T. Schlick,
``A Survey of Existing RNAs using Graph Theory with
Implications to RNA Analysis and Design,''
Nuc. Acids Res. 31: 2926--2943 (2003).
J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick,
``Structural Motifs in Ribosomal RNAs: Implications for RNA
Design and
Genomics,'' Biopolymers 73: 340--347 (2004).
H. H. Gan, D. Fera, J. Zorn, M. Tang, N. Shiffeldrim, U. Laserson,
N. Kim, and T. Schlick,``RAG: RNA-As-Graphs Database --
Concepts, Analysis, and Features,'' Bioinformatics 20: 1285--1291
(2004).
U. Laserson, H. H. Gan, and T. Schlick, ``Searching for 2D RNA
Geometries
in Bacterial Genomes,'' Proceedings of the ACM Symposium on
Computational Geometry, June 9--11, New York, pp. 373--377 (2004).
(http://socg.poly.edu/home.htm).
N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick,
``Novel Candidates of RNA Topologies,''
J. Mol. Biol. 341: 1129--1144 (2004).
Schlick, ``RAG: RNA-As-Graphs Web Resource,'' BMC Bioinformatics
5: 88--97
(2004)
(http://www.biomedcentral.com/1471-2105/5/88).
S. Pasquali, H. H. Gan, and T. Schlick, ``Modular RNA
Architecture Revealed
by Computational Analysis of Existing Pseudoknots and Ribosomal
RNAs,''
Nucl. Acids Res., Submitted (2004).
T. Schlick, Molecular Modeling: An Interdisciplinary Guide,
Springer-Verlag, New York, 2002.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2005.MAR.B7.1