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The Second q-bio Conference on Cellular Information Processing

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The q-bio Conference is not affiliated with arXiv.q-bio, but symbiotically coordinates with it.

Contents

Important announcements

Dates and Venue

Participants

Additional Information

Program

Pre-conference Events

  • q-bio Summer School in Los Alamos, July 21-August 5

Wednesday, Aug 6, 2008

12:45-17:00 Tutorials
  • Fireside Lounge
13:00-17:00 - Tutorial: Developing multi-cell developmental and biomedical simulations with CompuCell3D, Maciej Swat (Indiana University)
  • Classroom I
12:45-14:45 - Tutorial: Mathematical methods for systems biology, Eric Mjolsness (University of California, Irvine)
15:00-17:00 - Tutorial: Rule-based modeling of biochemical systems with BioNetGen, James R. Faeder (University of Pittsburgh School of Medicine), G. Matthew Fricke (University of New Mexico), William S. Hlavacek (Los Alamos National Laboratory), Bin Hu (University of New Mexico), Michael I. Monine (Los Alamos National Laboratory), and Ambarish Nag (Los Alamos National Laboratory)
  • Classroom II
13:00-14:45 - Tutorial: SimBiology, Ricardo Paxson (The MathWorks, Inc.)
15:00-16:45 - Tutorial: Bridging data and modeling communities: ontologies of cellular networks, pathway databases, and pathway data retrieval tools, Oliver Ruebenacker (University of Connecticut Health Center)
  • Classroom III
14:15-17:00 - Tutorial: Stochastic Gene Expression in Systems Biology, Mustafa H. Khammash (University of California, Santa Barbara) and Brian Munsky (Brian's slides) (Los Alamos National Laboratory)
  • Classroom IV
15:00-16:45 - Tutorial: Linking models to data and experimental predictions via SB-Pipeline, Arthur Goldsipe (Massachusetts Institute of Technology), Gerard Ostheimer (Massachusetts Institute of Technology) and Julio Saez-Rodriguez (Harvard Medical School)
17:00-17:45 Reception
17:45-19:45 Opening Banquet (Great Hall)
17:45-17:50 Welcome, Ilya Nemenman (Organizer, Los Alamos National Laboratory)
17:50-18:00 Welcome, Robert Ecke (Director, Center for Nonlinear Studies, Los Alamos National Laboratory)
18:00-19:00 Dinner
19:00-19:45 Bacterial Chemotaxis: Then and Now, Howard C. Berg (Harvard University), Dr. Berg will be introduced by Alan S. Perelson (Los Alamos National Laboratory)

Thursday, Aug 7, 2008

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30
08:30-12:10 Session I - Ilya Nemenman (chair)
08:30-09:00 All Politics is Local: Length Scales of the Coexistence of Competing Bacterial Strains In a Microhabitat Landscape, Robert H. Austin, Princeton University
09:00-09:20 Contributed Talk: Artificial nanopores that mimic the transport selectivity of the nuclear pore complex, Tijana Jovanovic-Talisman, Rockefeller University
09:20-09:50 Single-Molecule Approach to Molecular Biology in Living Bacterial Cells, X. Sunney Xie, Harvard University
09:50-10:10 Contributed Talk: Whole-genome in vivo monitoring of protein-DNA interactions in Escherichia coli, Tiffany Vora, American University in Cairo
10:10-10:35 Coffee Break
10:35-10:50 Poster Spotlights
Modeling the genetic dual-feedback oscillator, Matthew R. Bennett, University of California, San Diego
IL-2 couples T lymphocytes in their activation: from single cell to population, Ofer Feinerman, Memorial Sloan-Kettering Cancer Center
Gene-gene cooperativity in small networks, Aleksandra M. Walczak, Princeton University
A Computational Model for Bacterial Swarming, Yilin Wu, University of Notre Dame
10:50-11:20 Diffusion in Nanostructures: Counter-intuitive analytical results and supporting experiments, Sergey M. Bezrukov, National Institutes of Health
11:20-11:40 Contributed Talk: Cooperation in yeast sucrose metabolism, Jeff Gore, Massachusetts Institute of Technology
11:40-12:10 Design Principle of Adaptation Circuits, Chao Tang, University of California, San Francisco
12:10-14:00 Lunch
Dining Hall is open 11:30-1:30
14:00-18:00 Session II - James R. Faeder (chair)
14:00-14:30 Drug efflux deficiency promotes growth-bistability and target resistance masking among bacterial pathogens, Måns Ehrenberg, Uppsala University
14:30-15:00 Robustness of Yeast Cell Cycle under Stress Conditions, Edda Klipp, Max Planck Institute, Berlin
15:00-15:20 Contributed Talk: Signal Manipulation Coordinates Cellular Decision Making at the Population Level, Eric L. Haseltine, California Institute of Technology
15:20-15:50 Circadian Clocks and Switches in Cynanobacteria, Daniel S. Fisher, Stanford University
15:50-16:15 Coffee Break
16:15-16:30 Poster Spotlights
Experimental Design of In Vitro DNA Reaction Networks, Daniel Georgiev, University of Washington
Single-cell Study of Bacterial Signaling in Quorum Sensing, Tao Long, Princeton University
Implications of Dynamic Scaffolding for Signaling Efficiency in Drosophila Phototransduction, Stephen J. Helms, University of Texas Southwestern Medical Center at Dallas
Expression Variability from a Tet-inducible Positive Feedback Network in Mammalian Cells, Diane Longo, University of California, San Diego
16:30-17:00 TBD, Peter K. Sorger, Harvard Medical School
17:00-17:20 Contributed talk: Frequency-Modulated Localization Bursts Coordinate Gene Regulation, Long Cai, California Institute of Technology
17:20-17:50 Remarks on Interconnections, Modularity, and Dynamics, Eduardo D. Sontag, Rutgers
18:00-20:30 Dinner
20:30-23:00 Poster Session 1 List of posters: Thursday, August 7, 2008

Friday, Aug 8, 2008

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30
08:30-12:10 Session III - William S. Hlavacek (chair)
08:30-09:00 Metabolomics and Systems Biology, Masaru Tomita, Keio University
09:00-09:20 Contributed Talk: Fusion vs. endocytosis in receptor/coreceptor-mediated entry of enveloped viruses, Sarah Nowak, University of California, Los Angeles
09:20-09:50 TBD, Timothy S. Gardner, Amyris Biotechnologies
09:50-10:10 Contributed Talk: A single-cell view of multiple antibiotic resistance in Escherichia coli, Călin Guet, University of Chicago
10:10-10:35 Coffee Break
10:35-10:50 Poster Spotlights
How does a mast cell distinguish between two different extracellular stimuli that cause the same extent of receptor cross-linking?, Ambarish Nag, Los Alamos National Laboratory
Dynamics of p53 in non-stressed conditions, Alexander Loewer, Harvard Medical School
An integrated analytic model of bacterial chemotaxis, William Pontius, Yale University
Scalable learning of large networks, Sushmita Roy, University of New Mexico
10:50-11:20 Modeling aspects of solid cancer growth, Philip K. Maini, University of Oxford
11:20-11:40 Contributed Talk: From Molecule to Morphology: A Multi-Scale Cell-Based Model of Angiogenesis, Amy L. Bauer, Los Alamos National Laboratory
11:40-12:10 Proteomic and metabolomic analysis of nitrogen stress in Chlamydomonas reinhardtii, Oliver Fiehn, University of California, Davis
12:10-14:00 Lunch
Dining Hall is open 11:30-1:30
14:00-18:00 Session IV - Michael E. Wall (chair)
14:00-14:30 Integration of dynamic protein localization, proteolysis, and phospho-signaling drives transcriptional cell cycle circuitry, Lucy Shapiro, Stanford University
14:30-15:00 Reverse engineering the bacterial cell’s control system, Harley H. McAdams, Stanford University
15:00-15:20 Contributed Talk: The R8 Race: Patterning neurogenesis during Drosophila development, David K. Lubensky, University of Michigan
15:20-15:50 Molecular Mechanisms of Self-Assembly and Protein Export of the Bacterial Flagellum, Keiichi Namba, Osaka University
15:50-16:15 Coffee Break
16:15-16:30 Poster Spotlights
On the origin of symmetry in biological macromolecules, Charles E. M. Strauss, Los Alamos National Laboratory
Regulation of Integrin Clustering: Models and Experiments, Erik S. Welf, University of Delaware
The First Crystal Structure of cyclic GMP-dependent protein kinase Iβ dimerization domain reveals the molecular features of an extended leucine/isoleucine zipper, Choel Kim, University of California, San Diego
Quantitatively monitoring the G1 stability in single cell, Xiaojing Yang, University of California, San Francisco
16:30-17:00 Coordinate Regulation of G Protein Signaling via Dynamic Interactions of Receptor and GAP, Elliott M. Ross, University of Texas Southwestern Medical Center at Dallas
17:00-17:30 Specificity and reliability in biochemical networks, Peter S. Swain, McGill University
17:30-18:00 Learning of regulatory modules and predictive models of global transcriptional dynamics: application to the extremophile Halobacterium NRC-1, Richard Bonneau, New York University
18:00-20:30 Dinner
20:30-23:00 Poster Session 2 List of posters: Friday, August 8, 2008

Saturday, Aug 9, 2008

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30
08:30-12:10 Session V - Yi Jiang (chair)
08:30-09:00 Gene Regulation: Single Molecule Physics in a Natural Context, Peter G. Wolynes, University of California, San Diego
09:00-09:30 TBD, James E. Ferrell Jr., Stanford University
09:30-09:50 Contributed Talk: Global Robustness of A Three Protein Circadian Oscillator, Jin Wang, Stony Brook University
09:50-10:20 Variable Signaling Team Sizes of Escherichia coli Chemoreceptors: A New Level of Adaptation, Ned S. Wingreen, Princeton University
10:20-10:50 Coffee Break
10:50-11:20 EGF Receptor-Centric Autocrine Circuits in Context-Dependent Cell Signal Processing, Douglas A. Lauffenburger, Massachusetts Institute of Technology
11:20-11:40 Contributed Talk: Variability and Robustness in T Cell Activation from Regulated Heterogeneity in Protein Levels, Grégoire Altan-Bonnet, Memorial Sloan-Kettering Cancer Center
11:40-12:10 Bacterial growth control and the control by bacterial growth, Terence Hwa, University of California, San Diego
12:10-14:00 Lunch
Dining Hall is open 11:30-1:30
14:10-18:00 Session VI - Orna Resnekov (chair)
14:00-14:30 Quantitative analysis of endocytosis and cytokinesis, Thomas D. Pollard, Yale University
14:30-15:00 Cell lineages and the logic of proliferative control, Arthur D. Lander, University of California, Irvine
15:00-15:20 Contributed Talk: MAPK-dependent negative feedback in yeast pheromone response regulates system information transmission, Richard C. Yu, Molecular Sciences Institute
15:20-15:50 Regulation of VLA-4 integrin affinity and conformation by G protein-coupled receptor signaling pathways, Larry A. Sklar, University of New Mexico Health Sciences Center
15:50-16:30 Coffee Break
16:30-17:00 Plasma Membrane Heterogeneity and Receptor Mediated Signaling, Barbara Baird, Cornell University
17:00-17:30 Information Processing by Bacterial Cells: Beyond First Approximations, Ido Golding, University of Illinois, Urbana-Champaign
17:30-18:00 Diverse mechanisms of transcriptional activation in the Escherichia coli marA/soxS/rob regulon, Michael E. Wall, Los Alamos National Laboratory
18:00-18:30 Break
18:30-20:45 Closing Banquet (Dining Hall)
18:30-18:40 Farewell, Organizers
18:40-19:40 Dinner
19:40-19:45 Introduce banquet speaker
19:45-20:45 Closing Banquet Talk, Adam P. Arkin, Lawrence Berkeley National Laboratory

Post-conference Events

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