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2008-09 Program on Algebraic Methods in Systems Biology and StatisticsTutorials and Opening WorkshopSeptember 14-17, 2008
General Information
General InformationThe Opening Workshop for the SAMSI program on Algebraic Methods in Systems Biology and Statistics will be held on Sunday-Wednesday, September 14-17, 2008, at the Radisson Hotel RTP in Research Triangle Park, NC. On Sunday, September 14, tutorials will be offered on various applications of algebra in biology and statistics. From Monday to Wednesday, invited speakers will give presentations. We will also have a poster session.
The goals of the Opening Workshop are to take advantage of community input in the formation of the working groups for the program and to promote engagement in person or remotely, via web or teleconference for those not in residence at SAMSI during the program.
The workshop program will focus on the development and use of a particular set of tools from algebra, algebraic geometry, and discrete mathematics to solve problems in statistics and biology. A fundamental component of the workshop will take place during the afternoon of Wednesday, September 17, with the formation of working groups who will pursue research during the remainder of the program.
Program Committee: Reinhard Laubenbacher (Virginia Tech: Chair), Seth Sullivant (North Carolina State University), Brett Tyler (Virginia Tech), Rudy Yoshida (University of Kentucky)
ApplicationThe on-line application process is now closed.
Schedule
Sunday, September 14, 2008
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| 11:15-Noon | Registration |
| 12:00-1:00 | Lunch |
| 1:00-2:15 | An Invitation to Algebraic Statistics Homework Assignment Bernd Sturmfels, University of California, Berkeley |
| 2:15-2:30 | Break |
| 2:30-3:45 | An Introduction to Systems Biology Reinhard Laubenbacher, Virginia Bioinformatics Institute |
| 3:45-4:00 | Break |
| 4:00-5:15 | Phylogenetics Elizabeth Allman, University of Alaska |
Monday, September 15, 2008
Radisson Hotel RTP
| 8:00-8:45 | Registration and Continental Breakfast |
| 8:45-9:00 | Welcome |
| 9:00-9:45 | Algebraic Statistical Models Mathias Drton, University of Chicago |
| 9:45-10:00 | Questions and Discussions |
| 10:00-10:45 | The Geometry of Multisite Phosphorylation Jeremey Gunawardena, Harvard University |
| 10:45-11:00 | Questions and Discussions |
| 11:00-11:15 | Coffee Break |
| 11:15-Noon | Combinatorial Insights into RNA Folding Christine Heitsch, Georgia Institute of Technology |
| Noon-12:15 | Questions and Discussions |
| 12:15-1:30 | Lunch |
| 1:30-2:15 | Algebra, Automata, Algorithms, Biology and Beyond Bud Mishra, Courant Institute, New York University |
| 2:15-2:30 | Questions and Discussions |
| 2:30-3:15 | Reverse Engineering Nested Canalyzing Boolean Networks Abdul Jarrah, Virginia Bioinformatics Institute |
| 3:15-3:30 | Questions and Discussions |
| 3:30-3:45 | Break |
| 3:45-4:30 | Species and Genomes: Lessons from my Favorite Symbionts Chris Schardl, University of Kentucky |
| 4:30-4:45 | Questions and Discussions |
| 4:45-6:00 | Panel Discussion: Jeremy Gunawardena, Harvard University Ina Hoeschele, Virginia Polytechnic Institute Alexander Hartemink, Duke University Greg Rempala, Medical College of Georgia Brett Tyler, Virginia Polytechnic Institute |
| 6:00-6:30 | Poster Advertisement Session (2 minute ads each) |
| 6:30-8:30 | Poster Session and Reception SAMSI will provide poster presentation boards and tape. The board dimensions are 4 ft. wide by 3 ft. high. They are tri-fold with each side being 1 ft. wide and the center 2 ft. wide. Please make sure your poster fits the board. The boards can accommodate up to 16 pages of paper measuring 8.5 inches by 11 inches. |
Tuesday, September 16, 2008
Radisson Hotel RTP
| 8:15-9:00 | Registration and Continental Breakfast |
| 9:00-9:45 | Algebraic Structure of System Design Space for Metabolic Pathways and
Gene Circuits Michael Savageau, University of California, Davis |
| 9:45-10:00 | Questions and Discussions |
| 10:00-10:45 | Polynomial Equations and Instabilities in Biochemical Reaction Networks Gheorghe Craciun, University of Wisconsin |
| 10:45-11:00 | Questions and Discussions |
| 11:00-11:15 | Coffee Break |
| 11:15-Noon | Algebraic Geometry, Empirical Process, and Singular Model Evaluation Sumio Watanabe, Tokyo Institute of Technology |
| Noon-12:15 | Questions and Discussions |
| 12:15-1:30 | Lunch |
| 1:30-2:15 | Using Gröbner Bases to Reconstruct Regulatory Models in C. elegans Brandy Stigler, Mathematical Biosciences Institute |
| 2:15-2:30 | Questions and Discussions |
| 2:30-3:15 | Algebraic Combinatorics for Predicting Virus Assembly Pathways Meera Sitharam, University of Florida |
| 3:15-3:30 | Questions and Discussions |
| 3:30-3:45 | Break |
| 3:45-4:30 | The Algebra and Statistics of Biological Sequence Alignment Lior Pachter, Univ. of California-Berkeley |
| 4:30-4:45 | Questions and Discussions |
| 4:45-6:00 | Panel Discussion: Bernd Sturmfels, University of California, Berkeley Seth Sullivant, North Carolina State University Rudy Yoshida, University of Kentucky Peter Beerli, Florida State University Elizabeth Allman, University of Alaska |
Wednesday, September 17, 2008
Radisson Hotel RTP
| 8:15-9:00 | Registration and Continental Breakfast |
| 9:00-9:45 | Inferring Genetic Regulatory Networks in Host-Pathogen Interactions Brett Tyler, Virginia Polytechnic University |
| 9:45-10:00 | Questions and Discussions |
| 10:00-10:45 | Mathematical Models of Evolutionary Escape Niko Beerenwinkel, ETH Zurich |
| 10:45-11:00 | Questions and Discussions |
| 11:00-11:15 | Coffee Break |
| 11:15-Noon | Classes of Discrete Causal Models Eva Riccomagno, Università di Genova |
| Noon-12:15 | Questions and Discussions |
| 12:15-1:30 | Lunch |
| 1:30-2:15 | Algebraic Statistics for p1 Random Graph Models: Markov Bases and Their Uses Stephen Fienberg, Carnegie Mellon University |
| 2:15-2:30 | Questions and Discussions |
| 2:30-2:45 | Break |
| 2:45-5:00 | Break-out Sessions for Working Groups |
(Thursday and Friday: Possible working group meetings at SAMSI.)
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