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Program Information

The program for the accompanied AMS session March 10--11 is posted at:

Monday, March 12, 2012 (BSN 115):

Session: introduction to viruses (Chair: N. Jonoska)

9-10 Peter Stockley, University of Leeds, UK
Outwitting the viral machines: A joint challenge for biology, physics and mathematics.

10-10:30 Reidun Twarock, University of York UK
Viruses and geometry - where symmetry meets function

10:30: BREAK (poster set-up)

Sesssion: assembling viral capsids (Chair: R. Twarock)

11-11:30 -Giuliana Indelicato, University of York, UK
Non-icosahedral pathways for the expansion of icosahedral viral capsids: a coarse grained model

11:30-12 -Meera Sitharam, University of Florida, USA
Isolating crucial interactions in virus assembly by approximate configurational entropy using EASAL

12-12:30 -Mavis Agbandje-McKenna, University of Florida, USA
Defining VP-VP interactions that drive capsid assembly for Adeno-associated viruses

12:30-2 LUNCH

Session: sequence analysis (Chair: A. Carbone)

2-3 -Michael Savageau, University of California, Davis, USA
A generic characterization of phenotypic repertoire

3-3:30 -David Murrugarra, Virginia Bioinformatics Institute, USA
Understanding the effect of intrinsic noise in stability: a discrete approach

3:30 BREAK (poster viewing)

Session: secondary structure (Chair: T. Muche)

4-4:30 -Svetlana Poznanovikj, Georgia Institute of Technology, USA
Asymptotic enumeration of substructures in a stochastic context-free grammar model of RNA folding

4:30-5 -Massa Shoura, University of Texas, Dallas, USA
Measurements of DNA-loop formation via Cre-mediated recombination

5-5:30 -Susan Schroeder - University of Oklahoma USA
Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints

5:30-5:50 -Shel Swenson, Georgia Institute of Technology, USA
Profiling RNA secondary structures


Tuesday, March 13, 2012 (BSN 115)

Session: bio networks (Chair: K. Rejniak)

9-10 -Reinhard Laubenbacher,Virginia Bioinformatics Institute, USA
Algebraic models in systems biology

10-10:30 -Gheorghe Craciun University of Wisconsin-Madison, USA
Graph-theoretic criteria for multistability and persistence in biological networks

10:30 BREAK (poster viewing)

Session: packaging in confined space (Chair: A. Carbone)

11-11:30 -Przemyslaw Prusinkiewicz, University of Calgary, Canada
Constraints of space in plant development

11:30-12 -Yuanan Diao University of North Carolina - Charlotte, USA
Generating equilateral random polygons in confinement

12-12:30 -Eric Dykeman, University of York, UK
Using graph theory to identify genome organization and packaging mechanisms in ssRNA viruses

12:30-1:30pm LUNCH (shorter break than Monday or Wednesday)

Session: introduction to DNA topology (Chair: M. Saito)

1:30-2:30 -Isabel Darcy, University of Iowa, USA
Tutorial: Introduction to DNA topology

2:30-3 -Dorothy Buck, Imperial College London, UK
The classification of rational subtangle replacements, with applications to complex Nucleoprotein Assemblies

3-3:30 -Koya Shimokawa, Saitama University, Japan
Tangle analysis of unlinking by XerCD-diff-FtsK system

3:30 BREAK

Session: software tools (Chair: J. Burns)

4-4:30 -Robert Scharein, Hypnagogic Software, Canada
Computational knot theory with KnotPlot

4:30-5 -Brian Wolfe , California Institute of Technology, USA
NUPACK: analysis and design of nucleic acid system

5-5:30 -Egor Dolzhenko, University of South Florida, USA
STAGR: software to annotate genome rearrangement


Wednesday, March 14, 2012 (BSN 115)

Session: molecular rearrangements (Chair: E. Dolzhenko)

9-9:30 -Laura Landweber, Princeton University, USA
Radical genome architectures in Oxytricha

9:30-10 -Guénola Drillon Université Pierre et Marie Curie, France
Combinatorics of Chromosomal Rearrangements

10-10:30 -Karin Valencia, Imperial College London, UK
Topological characterization of knots and links arising from site-specific recombination on twist knot substrates.

10:30 BREAK

Session: evolutionary protein/nucleic acid interactions (Chair: R. Twarock)

11-11:30 -Alessandra Carbone, Université Pierre et Marie Curie, France
Combinatorial methods to extract co-evolution signals among residues in proteins Carbone (comb methods for residues in proteins)

11:30-12 -Aaron Goldman, Princeton University, USA
A systems biology approach to the origin of life and early metabolism

12-12:30 -Mary Therese Padberg, University of Iowa, USA
Exploring the conformations of protein-bound DNA: adding geometry to known topology

12:30-2pm LUNCH

2:00 PANNEL(Open Problems, discussions)
(Suggested) Panelists: Carbone, Bonizzoni, Buck, Daley, Laubenbacher, Stockley, Twarock

Workshop Dinner

The Monday night dinner will be at MOSI (Museum of Science and
Industry) which is about 15-20 minutes walk from the workshop venue.
We will try to have several rounds of driving to make sure that
everybody will make it. The dinner arrangement includes free entrance
to all regular exhibits at the museum.