The First q-bio Conference: Program

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Back to The First q-bio Conference. You may also want to view the program of the associated Summer School.

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



A report on the First q-bio Conference was published in Molecular Systems Biology (pdf).



Additional Information

Conference Program

Wednesday, Aug 8, 2007

14:00-16:15 Tutorials and Software Demonstrations
14:00-15:00 - Tutorial: Complex Systems Biology: In search of Universal Statistical Dynamics in Reproduction, Adaptation, and Phenotypic Evolution, Kunihiko Kaneko (University of Tokyo)
15:15-16:15 - Tutorial: Rule-based modeling using BioNetGen and the Virtual Cell, Michael Blinov (University of Connecticut Health Center)
17:00-17:45 Reception
17:45-19:45 Opening Banquet (Great Hall)
17:45-17:50 Welcome, Robert Ecke (Director, CNLS, Los Alamos National Laboratory)
17:50-18:00 Welcome, David H. Sharp (Chief Scientific Officer, Los Alamos National Laboratory)
18:00-19:00 Dinner
19:00-19:45 Searching for principles, William Bialek (Princeton University)

Thursday, Aug 9, 2007

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30
08:30-12:15 Session I - James R. Faeder (chair)
08:30-09:00 Physiology and genetic regulation of cellular signal transmission, Roger Brent (Molecular Sciences Institute)
09:00-09:20 Contributed Talk: Study of Signal Processing in Quorum Sensing at Single-Cell Level, Tao Long (Princeton University)
09:20-09:50 The Virtual Cell project, Leslie M. Loew (University of Connecticut Health Center)
09:50-10:20 Regulatory genome information processing during early development in the sea urchin, Smadar Ben-Tabou De-Leon (California Institute of Technology)
10:20-10:45 Coffee Break
10:45-10:55 Poster Spotlights
Modeling the Oscillatory Response of the NF-κB Signaling Pathway, Diane Longo (UC San Diego)
How Cells Decide Between Apoptosis and Survival in Response to DNA Damage, Gerry Ostheimer (MIT)
Switching gene-regulatory loops in Th1 differentiation, Edda Schulz (Humboldt)
10:55-11:25 Optimization of the cellular response and searching strategy in bacterial chemotaxis, Thierry Emonet (Yale)
11:25-11:45 Contributed Talk: Live Cell Imaging Methods to Quantify Signaling Molecule Dynamics, Diane Lidke (UNM)
11:45-12:15 Systems biology of the Drosophila blastoderm: what can we learn?, John Reinitz (Stony Brook University)
12:15-14:00 Lunch
Dining Hall is open 11:30-1:30
14:00-17:45 Session II - William S. Hlavacek (chair)
14:00-14:30 Investigating a temporal code of inflammatory signaling, Alexander Hoffmann (UC San Diego)
14:30-14:50 Contributed Talk: Metabolic gene regulation in a dynamically changing environment, Matthew Bennett (UC San Diego)
14:50-15:20 Specificity in Bacterial Two-Component Signaling, Mark Goulian (University of Pennsylvania)
15:20-15:50 Reconstruction of the genome-scale transcriptional regulatory network in E. coli, Bernhard Ø. Palsson (University of California, San Diego)
15:50-16:15 Coffee Break
16:15-16:25 Poster Spotlights
Activating Ras Mutations in vitro and in Cancer, Edward Stites (U of Virginia) Fangping Mu (LANL)
Probabilistic Modeling & Analysis of Switch-Like Signal Transduction Systems, Marc Birtwistle (University of Delaware)
Quantitative assessment of endothelial cell response to spatial gradients of VEGF, David Noren (Johns Hopkins U)
16:25-16:55 Signaling through cAMP and cAMP-dependent Protein Kinase, Susan Taylor (UC San Diego)
16:55-17:15 Contributed Talk: Engineering the Salmonella SPI-1 System for Heterologous Protein Production, Danielle Tullman-Ercek (UC San Francisco)
17:15-17:45 Exploring the Design Space of MAP Kinase Cascades, Noah Helman (UC San Francisco)
17:45-20:15 Dinner
charter bus service to downtown locations
20:15-22:45 Poster Session 1

Friday, Aug 10

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30
08:30-12:15 Session III - Michael E. Wall (chair)
08:30-09:00 Engineered Gene Circuits, Jeff Hasty (University of California, San Diego)
09:00-09:20 Contributed Talk: Correlation and Causality in Genetic Networks, Mary Dunlop (Caltech)
09:20-09:50 Systems Behavior in Phage λ and Evolution of Complex Regulatory Circuitry, John W. Little (University of Arizona)
09:50-10:20 Quantifying Biological Performance in System Design Space, Michael A. Savageau (University of California, Davis)
10:20-10:45 Coffee Break
10:45-10:55 Poster Spotlights
Open Complex Formation by Bacterial RNA Polymerase - a Quantitative Model, Marko Djordjevic (Ohio State)
Stochastic model for IL-4 expression dynamics, Luca Mariani (Humboldt U)
Physical theory of nucleo-cytoplasmic transport, Anton Zilman (LANL)
10:55-11:25 Pre-Existing Variation Controls the Lysis-Lysogeny Decision in Phage Lambda Infection, Drew Endy (Massachusetts Institute of Technology)
11:25-11:45 Contributed Talk: Variability dynamics of protein levels in human cells, Alex Sigal (Caltech)
11:45-12:15 Casting a Net for Kinases - Probabilistic Modeling of Cellular Signaling Systems, Rune Linding (Samuel Lunenfeld Research Institute)
12:15-14:00 Lunch
Dining Hall is open 11:30-1:30
14:00-17:45 Session IV - Yi Jiang (chair)
14:00-14:30 Mapping and modeling receptor topography during signal transduction, Bridget S. Wilson (University of New Mexico)
14:30-14:50 Contributed Talk: Finite State Projection Solutions to the CME Arising in Gene Regulatory Networks, Brian Munsky (UCSB)
14:50-15:20 Dynamics of signal transduction and gene expression in single cells, Alexander van Oudenaarden (Massachusetts Institute of Technology)
15:20-15:50 How to move through a very dense crowd, Dale Kaiser (Stanford University)
15:50-16:15 Coffee Break
16:15-16:25 Poster Spotlights
Fly Magnetism: Planar cell polarity in the wing, Yoram Burak (UC Santa Barbara)
Coarse-graining biochemical reactions, Nikolai Sinitsyn (LANL)
Quantitative Analysis of HER2 Overexpression Effect on EGF Receptor Signaling, Yi Zhang (PNNL)
16:25-16:55 Optimal path to epigenetic switching, Anirvan Sengupta (Rutgers)
16:55-17:15 Contributed Talk: Sensitivity, feedback and fluctuations in bacterial chemotaxis, Thomas Shimizu (Harvard University)
17:15-17:45 Trade-offs and limits in feedback-driven noise suppression, Johan Paulsson (Harvard Medical School)
17:45-20:15 Dinner
Charter bus service to downtown locations
20:15-22:45 Poster Session 2

Saturday, Aug 11, 2007

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30
08:30-12:15 Session V - Ilya Nemenman (chair)
08:30-09:00 Information processing by gradient sensing system: convergence of methods, divergence of means, Andre Levchenko (Johns Hopkins University)
09:00-09:20 Contributed Talk: Form, Function, and Information Processing in Small Stochastic Biological Networks, Chris Wiggins (Columbia University)
09:20-09:50 Adaptation of genetic regulatory networks and its role in cell evolvability, Naama Brenner (Technion-Israel Institute of Technology)
09:50-10:20 (De)constructing cellular networks, Adam P. Arkin (Lawrence Berkeley National Laboratory)
10:20-10:45 Coffee Break
10:45-11:15 Stochastic dynamics of macromolecular-assembly networks, Jose M. G. Vilar (Sloan-Kettering Institute)
11:15-11:45 From molecules to behavior: Understanding responses of E. coli to complex temporal signals, Yuhai Tu (IBM T.J. Watson Research Center)
11:45-12:15 Systematic Analysis of Crosstalk in the PDGF Receptor Signal Transduction Network, Jason M. Haugh (North Carolina State University)
12:15-14:00 Lunch
Dining Hall is open 11:30-13:30
14:00-18:15 Session VI - Byron Goldstein (chair)
14:00-14:30 Probing Transcription Factor Dynamics at the Single Molecule Level in a Living Cell, Johan Elf (Harvard University)
14:30-15:00 How T cells see antigen, Arup K. Chakraborty (Massachusetts Institute of Technology)
15:00-15:20 Contributed Talk: Applications of sensitivity analysis for drug discovery and development in the ErbB network, Birgit Schoeberl (Merrimack Pharmaceuticals)
15:20-15:50 Graph Theory Based Hypotheses with Experimental Validation to Identify Novel Functions of Components and Pathways in Mammalian Cells, Avi Ma'ayan (Mount Sinai School of Medicine)
15:50-16:15 Coffee Break
16:15-16:45 Cell Signaling Dynamics in Time and Space, Boris N. Kholodenko (Thomas Jefferson University)
16:45-17:15 Quantitative phosphoproteomics in cell signaling, Blagoy Blagoev (University of Southern Denmark)
17:15-17:45 Autocrine signaling and feedback loops in the EGF receptor system, H. Steven Wiley (Pacific Northwest National Laboratory)
17:45-18:15 Rule-based modeling of signal-transduction systems, James R. Faeder (University of Pittsburgh School of Medicine)
18:15-18:45 Break
18:45-20:45 Closing Banquet (Dining Hall)
18:45-19:00 Farewell, Organizers
19:00-20:00 Dinner
20:00-20:45 Rules of engagement: The architecture of robust, evolvable networks, John Doyle (California Institute of Technology) Slides
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