Organizers:
Gheorghe Craciun	Mathematics and Biomolecular Chemistry, University of Wisconsin-Madison
Thomas G. Kurtz	Mathematics and Statistics, University of Wisconsin-Madison
Lea Popovic	Mathematics and Statistics, Concordia University
Grzegorz A. Rempala	Mathematics and Biochemistry and Molecular Biology, University of Louisville
Ruth Williams	Mathematics, University of California-San Diego
John Yin	Chemical and Biological Engineering, University of Wisconsin-Madison

With the completion of numerous genome projects for bacteria, yeast, and humans, there is an increasing interest in understanding how molecules encoded within the genomes interact to define various functional networks of the cell. These intra-cellular networks may be classified as gene regulatory networks, protein interaction networks, or metabolic networks. Such networks of integrated molecular reactions tend to involve many different molecular species, thus posing complex analytical problems. For prediction and simulation purposes it is essential to reduce both the model and computational complexity of the problem, while still capturing all the essential characteristics and potential behavior of the network. This workshop will summarize some of the new and classical approaches to developing stochastic models for chemical reaction networks, beginning with Markov chain models and proceeding to some more recent ones which take into account the stepwise development of reactions involving RNA and DNA molecules. The workshop will focus on the following topics:

• Stochastic models of reaction networks.
• Structural properties of reaction networks and the relationship between structural properties and system behavior.
• Simulation of high dimensional systems.
• Parameter estimation and model validation for complex stochastic models.

The workshop will be proceeded by a tutorial that will help participants develop the common base of knowledge that will make the workshop presentations accessible.

Sunday | Monday | Tuesday
Sunday May 11, 2008
Introductory lectures
12:00pm-1:00pm	Registration and coffee		EE/CS 3-176
1:00pm-1:15pm	Welcome and introduction	Chehrzad Shakiban (University of Minnesota)	EE/CS 3-180
1:15pm-2:15pm	Opening plenary talk: Stochastic analysis is the fundamental tool for understanding biological function	Michael Reed (Duke University)	EE/CS 3-180
2:15pm-2:30pm	Coffee		EE/CS 3-176
2:30pm-3:30pm	Models and measures of virus growth and infection spread	John Yin (University of Wisconsin-Madison)	EE/CS 3-180
3:30pm-4:00pm	Coffee		EE/CS 3-176
4:00pm-5:00pm	Analyzing stochastic models	Thomas Kurtz (University of Wisconsin-Madison)	EE/CS 3-180
5:00pm-5:30pm	Second chances		EE/CS 3-180
6:30pm-8:30pm	Workshop dinner		Caspian Bistro 2418 University Ave SE Minneapolis, MN 55414 612-623-1133
Monday May 12, 2008
8:30am-9:00am	Coffee		EE/CS 3-176
9:00am-10:00am	Subdiffusion and reaction networks in biophysics	Samuel Kou (Harvard University)	EE/CS 3-180
10:00am-10:30am	Coffee		EE/CS 3-176
10:30am-11:30am	Fundamental limits on the suppression of randomness in biology	Johan Paulsson (Harvard Medical School)	EE/CS 3-180
11:30am-1:15pm	Lunch		EE/CS 3-176
1:15pm-2:45pm	An introduction to discrete-event simulation	Peter Glynn (Stanford University) Peter Haas (IBM Research Division)	EE/CS 3-180
2:45pm-3:15pm	Coffee		EE/CS 3-176
3:15pm-3:45pm	Part I: Local and global stability of biochemical reaction network dynamics	Gheorghe Craciun (University of Wisconsin-Madison)	EE/CS 3-180
3:50pm-4:20pm	Part II: Homotopy methods for counting reaction network equilibria	Ruth Williams (University of California, San Diego)	EE/CS 3-180
4:20pm-4:50pm	Second chances		EE/CS 3-180
4:50pm-5:00pm	Group photo
5:00pm-6:30pm	Reception and Poster Session Lind Hall 400 Product form stationary distributions for deficiency zero chemical reaction networks David Anderson (University of Wisconsin-Madison) Solutions to inverse problems of biochemical networks using stochastic methods Mónica Bugallo (SUNY) Petar Djuric (SUNY) Interlaced Euler scheme for stiff stochastic differential equations Ioana Cipcigan (University of Maryland Baltimore County) Muruhan Rathinam (University of Maryland Baltimore County) Stochastic simulations of reaction-diffusion models Anilkumar Devarapu (University of Louisville) Simulating discrete biochemical reaction systems Arnab Ganguly (University of Wisconsin-Madison) Multiscale methods in a heat shock response model Hye-Won Kang (University of Wisconsin-Madison) Stochastic models for intracellular reaction networks Yiannis Kaznessis (University of Minnesota) Stochastic control analysis for biological reaction systems Kyung Kim (University of Washington) Predicting translation rate from sequence Howard Salis (University of California, San Francisco) Stochastic modeling of vesicular stomatitis virus(VSV) growth in cells: An application of order statistics to predict replication delays Rishi Srivastava (University of Wisconsin-Madison) Stochastic modeling of bistable chemical systems: Schlogl's model Melissa Vellela (University of Washington) Biochemical and network modeling of the mammalian suprachiasmatic nucleus Richard Yamada (University of Michigan)
Tuesday May 13, 2008
8:15am-8:45am	Coffee		EE/CS 3-176
8:45am-9:45am	Stochastic oscillations in small genetic networks	Lev Tsimring (University of California, San Diego)	EE/CS 3-180
9:45am-10:45am	Multiscale models for synthetic biology	Yiannis Kaznessis (University of Minnesota)	EE/CS 3-180
10:45am-11:15am	Coffee		EE/CS 3-176
11:15am-12:15pm	Stochastic aspects of actin filament dynamics	Hans Othmer (University of Minnesota)	EE/CS 3-180
12:15pm-1:45pm	Lunch		EE/CS 3-180
1:45pm-2:45pm	Bayesian inference for stochastic intracellular reaction network models	Darren Wilkinson (University of Newcastle upon Tyne)	EE/CS 3-180
2:45pm-3:45pm	Inferring an underlying reaction network from the data	Grzegorz Rempala (University of Louisville)	EE/CS 3-180
3:45pm-4:15pm	Coffee		EE/CS 3-176
4:15pm-4:45pm	Second chances		EE/CS 3-180
4:45pm-5:45pm	Closing plenary talk: Metabolic engineering and metabolic modeling: where do we go from here?	James Liao (University of California, Los Angeles (UCLA))	EE/CS 3-180

NAME	DEPARTMENT	AFFILIATION
Claudio Altafini	Department of Functional Analysis and Applications	International School for Advanced Studies (SISSA/ISAS)
David Anderson	Department of Mathematics	University of Wisconsin-Madison
Ping Ao	Department of Mechanical Engineering	University of Washington
Douglas Arnold	Institute for Mathematics and its Applications	University of Minnesota
Banu Baydil	Department of Mathematical Sciences	Rensselaer Polytechnic Institute
Yermal Bhat	Institute for Mathematics and its Applications	University of Minnesota
Lisa Bishop	Department of Applied Mathematics	University of Washington
Khalid Boushaba	Department of Mathematics	Iowa State University
Maury Bramson	School of Mathematics	University of Minnesota
Mónica Bugallo	Department of Electrical and Computer Engineering	SUNY
Don Button	Marine Science/Biochemistry	University of Alaska
Maria-Carme Calderer	School of Mathematics	University of Minnesota
Yang Cao	Department of Computer Science	Virginia Polytechnic Institute and State University
Teng Chen	Department of Mathematics	University of Central Florida
Lauren Childs	Center for Applied Mathematics	Cornell University
Ioana Cipcigan	Department of Mathematics & Statistics	University of Maryland Baltimore County
Gheorghe Craciun	Department of Mathematics and Department of Biomolecular Chemistry	University of Wisconsin-Madison
Anilkumar Devarapu		University of Louisville
Lee DeVille	Department of Mathematics	University of Illinois at Urbana-Champaign
Ton Dieker	Thomas J. Watson Research Center	IBM
Kequan Ding		Chinese Academy of Sciences
Petar Djuric	Department of Electrical and Computer Engineering	SUNY
Walid Fakhouri	Department of Biochemistry and Molecular Biology	Michigan State University
Sergei Fedotov	School of Mathematics	University of Manchester
Christodoulos Floudas	Department of Chemical Engineering	Princeton University
John Fricks	Department of Mathematics	Pennsylvania State University
Arnab Ganguly	Mathematics Department	University of Wisconsin-Madison
Peter Glynn	Department of Management Science and Engineering	Stanford University
Paula Grajdeanu	Mathematical Biosciences Institute	Ohio State University
Peter Haas		IBM Research Division
Esfandiar Haghverdi	School of Informatics	Indiana University
Adam Halasz	Department of Mechanical Engineering	University of Pennsylvania
Anthony Hill		University of Minnesota
Hye-Won Kang	Department of Mathematics	University of Wisconsin-Madison
Yiannis Kaznessis	Department of Chemical Engineering and Materials Science	University of Minnesota
Kyung Kim	Department of Bioengineering	University of Washington
Dmitry Kondrashov	The Division of Biological Sciences	University of Chicago
Samuel Kou	Department of Statistics	Harvard University
Peter Kramer	Department of Mathematical Sciences	Rensselaer Polytechnic Institute
Thomas Kurtz	Department of Mathematics	University of Wisconsin-Madison
Yury Kutoyants	Laboratoire de Statistique et Processus	Université du Maine
Yueheng Lan	Department of Mechanical Engineering	University of California, Santa Barbara
Chang Lee	Department of Mathematical Sciences	Worcester Polytechnic Institute
James Liao	Department of Chemical and Biomolecular Engineering	University of California, Los Angeles (UCLA)
Di Liu	Department of Mathematics	Michigan State University
Hailiang Liu	Department of Mathematics	Iowa State University
Roger Lui	Department of Mathematical Sciences	Worcester Polytechnic Institute
M. David Marks	Department of Plant Biology	University of Minnesota
Scott McKinley	Mathematics Department	Duke University
Bence Melykuti	Department of Statistics	University of Oxford
Vicenc Mendez	Department of Physics	Autonomous University of Barcelona
Hitesh Mistry	Department of Mathematics	University of Dundee
Michael Monine	Department of Theoretical Biology and Biophysics	Los Alamos National Laboratory
Ambarish Nag	Theoretical Biology and Biophysics Department	Los Alamos National Laboratory
Timothy Newman	Department of Physics	Arizona State University
David Odde	Department of Biomedical Engineering	University of Minnesota
Hans Othmer	Department of Mathematics	University of Minnesota
Johan Paulsson	Department of Systems Biology	Harvard Medical School
Lea Popovic	Department of Mathematics & Statistics	Concordia University
Muruhan Rathinam	Department of Mathematics & Statistics	University of Maryland Baltimore County
Michael Reed	Department of Mathematics	Duke University
Grzegorz Rempala	Department of Mathematics	University of Louisville
Alexander Roitershtein	Department of Mathematics	Iowa State University
Howard Salis		University of California, San Francisco
Sebastian Sandersius	Department of Physics	Arizona State University
Deena Schmidt	Institute for Mathematics and its Applications	University of Minnesota
Chehrzad Shakiban	Institute of Mathematics and its Applications	University of Minnesota
Vassilios Sotiropoulos		University of Minnesota
Rishi Srivastava	Department of Chemical and Biological Engineering	University of Wisconsin-Madison
David Tello	Department of Mathematics & Statistics	Arizona State University
Lev Tsimring	Institute for Nonlinear Science	University of California, San Diego
Melissa Vellela	Department of Applied Mathematics	University of Washington
Jorge Vinals	Department of Physics	McGill University
Jin Wang	Department of Chemistry, Physics and Applied Mathematics	SUNY
Darren Wilkinson	School of Mathematics and Statistics	University of Newcastle upon Tyne
Ruth Williams	Department of Mathematics	University of California, San Diego
Zhijun Wu	Department of Mathematics	Iowa State University
Richard Yamada	Department of Mathematics	University of Michigan
John Yin	Department of Chemical and Biological Engineering	University of Wisconsin-Madison
Zhigang Zhang	Department of Mathematics	University of Houston