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The Third q-bio Conference on Cellular Information Processing

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The Third q-bio Conference on Cellular Information Processing is scheduled for August 5-9, 2009.

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

Important announcements

  • The program, including the poster sessions, has been finalized.
  • Early registration is closed, but registration at the door is still available.
  • Use The Ride Sharing Board to arrange transportation to the conference from the airport.

Dates and Venue

Additional Information

Participants

Satellite Meetings and Special Sessions

All satellite meetings and special sessions will be held on the afternoon of Friday, Aug 7, when the main conference breaks for sightseeing and impromptu discussions.

Program

Pre-conference Events

Wednesday, Aug 5, 2009

12:00-17:00 Tutorials
12:00-13:30 Oliver Ruebenacker, University of Connecticut Health Center, Retrieving pathway data for use in kinetic modeling
13:45-15:15 James R. Faeder, University of Pittsburgh School of Medicine, Rule-based modeling with BioNetGen
15:30-17:00 Ty M. Thomson, Plectix BioSystems, Inc., Modeling in Cellucidate: tackling complexity, communication and collaboration
17:00-17:30 Reception
17:45-19:50 Opening Banquet (Great Hall)
17:45-17:55 Welcome, Terry Wallace, Principal Associate Director for Science, Technology and Engineering, Los Alamos National Laboratory
17:55-18:00 Welcome, Robert Ecke, Director, Center for Nonlinear Studies, Los Alamos National Laboratory
18:00-19:00 Dinner
19:00-19:05 Introduction of Dr. Alberts, Hans Frauenfelder, Senior Laboratory Fellow, Los Alamos National Laboratory
19:05-19:50 Bruce Alberts, University of California, San Francisco, Biology past and biology future: where have we been and where are we going?

Thursday, Aug 6, 2009

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
08:30-12:10 Session I - Ilya Nemenman (chair)
08:30-09:00 Carlos Bustamante, University of California, Berkeley, Grabbing the cat by the tail: discrete steps by a DNA packaging motor and the inter-subunit coordination in a ring-ATPase
09:00-09:20 Contributed Talk: David Sprinzak, California Institute of Technology, Mutual inactivation of Notch and Delta amplifies differences between neighboring cells (pdf)
09:20-09:50 Andrea C. Vaiana, Max Planck Institute, Göttingen, Simulation of antibiotics that interfere with the ribosomal machinery
09:50-10:10 Contributed Talk: Savaş Tay, Stanford University, NF-κB signaling, dynamic range and stochastic switching under TNF and LPS stimulation (pdf)
10:10-10:35 Coffee Break
10:35-10:50 Poster Spotlights I
Rhys M. Adams, University of Texas M.D. Andersen Cancer Center, Design principles of synthetic gene circuits based on the TetR family of regulators (pdf)
Marcelo Behar, University of California, San Diego, Transfer of dynamically encoded information in the NF-κB signaling network (pdf)
Daniel Andor-Ardó, Rockefeller University, Biological oscillators with autocatalytic steps: resonant release of synaptic transmitter (pdf)
Andrew Mugler, Columbia University, Mesoscopic statistical properties of multistep enzyme-mediated reactions (pdf)
10:50-11:20 Aaron R. Dinner, University of Chicago, Signatures of regulatory synergies in intrinsic biological noise
11:20-11:40 Contributed Talk: Roee Amit, California Institute of Technology, Synthetic cis regulatory modules (pdf)
11:40-12:10 Pablo A. Iglesias, Johns Hopkins University, Information-theoretic characterization of signal transduction pathways
12:10-14:30 Lunch
Dining Hall is open 11:30 AM -1:30 PM for lunch
14:30-18:10 Session II - William S. Hlavacek (chair)
14:30-15:00 Byron Goldstein, Los Alamos National Laboratory, Assessing the role of serial engagement in mast cell signaling
15:00-15:20 Contributed Talk: Yaron E. Antebi, Weizmann Institute of Science, Collective decision making in T cells (pdf)
15:20-15:50 Thomas Gregor, Princeton University, Transition to collective behavior in eukaryotic cell populations
15:50-16:15 Coffee Break
16:15-16:30 Poster Spotlights II
Joshua Socolar, Duke University, Modeling cell fate specification in the sea urchin embryo (pdf)
Gabriele Lillacci, University of California, Santa Barbara, Parameter estimation and model selection in computational biology (pdf)
Pablo Meyer, Columbia University Medical School, Cellular organization of a metabolic pathway (pdf)
Golan Bel, Los Alamos National Laboratory, Specificity and first passage times of common biochemical processes (pdf)
16:30-17:00 Martha L. Bulyk, Harvard University, High-resolution DNA binding specificity profiles of transcription factors and cis regulatory codes in DNA
17:00-17:20 Contributed Talk: Smadar Ben-Tabou de-Leon, California Institute of Technology, The information processing at the foxa node of the sea urchin gene regulatory network (pdf)
17:20-17:50 Andrew H.A. Clayton, Ludwig Institute for Cancer Research, EGF receptor in the lime light
17:50-18:10 Contributed Talk: Christian L. Barrett, University of California, San Diego, Meta-structure of a bacterial genome (pdf)
18:10-20:30 Dinner (no cafeteria service)
20:30-23:30 Poster Session 1
Drinks and snacks will be served

Friday, Aug 7, 2009

07:30-09:00 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
09:00-12:00 Session III - James R. Faeder (chair)
09:00-09:30 Linda R. Petzold, University of California, Santa Barbara, Model reduction for chemical reaction networks: it’s a subtle business!
09:30-09:50 Contributed Talk: Lon Chubiz, University of Illinois, Urbana-Champaign, Coordinated regulation of multiple-antibiotic resistance in Escherichia coli (pdf)
09:50-10:20 Haw Yang, Princeton University, Cellular energy regulation from a single-molecule protein dynamics perspective
10:20-10:40 Coffee Break
10:40-11:10 Nir S. Gov, Weizmann Institute of Science, Ladders and ropes: active transport inside the stereocilia and other cellular protrusions
11:10-11:30 Contributed Talk: Julien O. Dubuis, Princeton University, Positional information, in bits (pdf)
11:30-12:00 Jin Zhang, Johns Hopkins University School of Medicine, Dynamic visualization of signaling activities in living cells
12:00 Break in the Regular Program
Dining Hall is open 11:30 AM -1:30 PM for lunch
14:00-17:45 Satellite Meeting, Biology on Demand, Junior Room - Ilya Nemenman and John P. Wikswo (co-organizers)
14:00-14:05 Ilya Nemenman, Los Alamos National Laboratory, Introduction
14:05-14:30 Fiona A. Chandra, California Institute of Technology, Theoretical performance limit of the autocatalytic glycolysis system (pdf)
14:30-14:55 Howard Salis, University of California, San Francisco, Predicting and controlling translation rate in bacteria (pdf)
14:55-15:20 Alex Groisman, University of California, San Diego, Quantitative studies of bacteria in microfluidic devices (pdf)
15:20-15:40 Coffee Break
15:40-16:05 Brian Munsky, Los Alamos National Laboratory, Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters (pdf)
16:05-16:30 David Thorsley, University of Washington, Observers for stochastic chemical kinetics (pdf)
16:30-16:55 Bryan C. Daniels, Cornell University, Statistical model selection and prediction of systems’ responses to exogenous perturbations (pdf)
16:55-17:20 Gabriele Lillacci, University of California, Santa Barbara, Parameter estimation and model selection in computational biology (pdf)
17:20-17:45 David Ellison, Johns Hopkins University, Computational model and microfluidic platform for the investigation of paracrine and autocrine signaling in mouse embryonic stem cells (pdf)
14:00-17:00 Special Session on Methods, Great Hall - William S. Hlavacek and Fangping Mu (co-chairs)
14:00-14:20 Alan Waggoner, Carnegie Mellon University, Fluorescent biosensors for cell regulation pathways (pdf)
14:20-14:40 Jeffrey R. Enders, Vanderbilt University, Microfluidic-ion mobility-mass spectrometry for assessing cellular response in real time (pdf)
14:40-15:00 Blagoy Blagoev, University of Southern Denmark, Unraveling ubiquitination dependent dynamics in cell signaling networks by quantitative proteomics (pdf)
15:00-15:20 Diane S. Lidke, University of New Mexico Cancer Center, Correlating FcεRI signaling with dynamics using single quantum dot imaging (pdf)
15:20-15:40 Coffee Break
15:40-16:00 James H. Werner, Los Alamos National Laboratory, Confocal, 3D tracking of individual quantum dot labeled signaling molecules on live cells (pdf)
16:00-16:20 Verena Wolf, Saarland University, Solving the chemical master equation using creeping windows (pdf)
16:20-16:40 Dragos Amarie, Indiana University, Microfluidics devices integrating microcavity surface plasmon resonance biosensors: glucose oxidase enzymatic activity (pdf)
16:40-17:00 Ying-Ja Chen, University of California, San Diego, Simulations and experiments for DNA sequencing by denaturation (pdf)

Saturday, Aug 8, 2009

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
08:30-12:00 Session IV - Yi Jiang (chair)
08:30-09:00 Rita R. Colwell, University of Maryland, Climate, oceans, infectious diseases, and human health: biocomplexity of cholera epidemics
09:00-09:20 Contributed Talk: Deborah A. Flusberg, Harvard Medical School, Single-cell heterogeneity and transient resistance in the apoptotic response to TRAIL (pdf)
09:20-09:50 Vito Quaranta, Vanderbilt University School of Medicine, Heterogeneity of cancer cell motility
09:50-10:10 Contributed Talk: Ambhighainath Ganesan, Johns Hopkins University, Using microfluidic device based experimentation to unravel the topology of a maltose sub-regulon (pdf)
10:10-10:35 Coffee Break
10:35-10:50 Poster Spotlights III
Dmitry Nevozhay, University of Texas M. D. Anderson Cancer Center, Precise regulation of gene expression by negative feedback (pdf)
Dean A. Tolla, University of California, Davis, Growth rate effects on global regulation of E. coli oxygen sensing (pdf)
Gašper Tkačik, University of Pennsylvania, Optimizing information flow in small genetic networks (pdf)
Chenghang Zong, University of Illinois, Urbana-Champaign, Predicting the stability of an epigenetic state (pdf)
10:50-11:10 Contributed Talk: Kazuzki Horikawa, Hokkaido University, Constructive role of noise in self-organized pattern formation in social amoeba (pdf)
11:10-11:40 Hiroki R. Ueda, RIKEN, Systems biology of mammalian circadian clocks
11:40-12:00 Contributed Talk: Ali Kinkhabwala, Max-Planck-Institut für molekulare Physiologie, Radio transmission in the cell (pdf)
12:00-14:30 Lunch
Dining Hall is open 11:30 AM - 1:30 PM for lunch
14:30-18:00 Session V - Janet M. Oliver (chair)
14:30-15:00 Nina V. Fedoroff, Pennsylvania State University, 21st Century science diplomacy
15:00-15:20 Contributed Talk: Linda J. Kenney, University of Illinois-Chicago, Towards a quantitative description of the EnvZ/OmpR two-component system during osmotic signaling (pdf)
15:20-15:40 Contributed Talk: Stephen J. Helms, University of Texas Southwestern Medical Center, Regulatory mechanisms of dynamic scaffolding in Drosophila phototransduction (pdf)
15:40-16:05 Coffee Break
16:05-16:20 Poster Spotlights IV
Aleksandra M. Walczak, Princeton University, Information processing in gene regulatory cascades (pdf)
Hyun Youk, Massachusetts Institute of Technology, Balancing sensing and uptake of glucose in yeast (pdf)
Philippos Tsourkas, University of California, Davis, Affinity discrimination in B cells requires kinetic proofreading (pdf)
Howard Salis, University of California, San Francisco, Predicting and controlling translation rate in bacteria (pdf)
16:20-16:50 Antony W. Burgess, Ludwig Institute for Cancer Research, Melbourne, Modeling Wnt signaling and colon cancer
16:50-17:10 Contributed Talk: Ganhui Lan, IBM T.J. Watson Research Center, Condensation of FtsZ filaments drives bacterial cell division (pdf)
17:10-17:40 Joern Dengjel, Freiburg Institute for Advanced Studies, Spatio-temporal protein dynamics during autophagy
17:40-18:00 Contributed Talk: Tatiana T. Marquez-Lago, Swiss Federal Institute of Technology (ETH) Zürich, Stochastic modeling of a tunable synthetic mammalian oscillater (pdf)
18:00-20:30 Dinner (no cafeteria service)
20:30-23:30 Poster Session 2
Drinks and snacks will be served

Sunday, Aug 9, 2009

07:30-09:00 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
09:00-12:00 Session VI - Michael E. Wall (chair)
09:00-09:30 Michael P. Sheetz, Columbia University, Shaping cells by force and rigidity through protein stretching
09:30-09:50 Contributed Talk: William Mather, University of California, San Diego, Dynamic pheromone gradient sensing in yeast (pdf)
09:50-10:20 Sander J. Tans, AMOLF, Evolutionary adaptation of regulation in variable environments
10:20-10:50 Coffee Break
10:50-11:10 Contributed Talk: Giovanni Meacci, IBM T.J. Watson Research Center, Intra- and intercellular fluctuations in Min protein dynamics decrease with cell age (pdf)
11:10-11:40 Gürol M. Süel, University of Texas Southwestern Medical Center, Dissecting the functional importance of gene circuit architecture
11:40-12:00 Contributed Talk: Sven Mesecke, German Cancer Research Center (DKFZ), Heidelberg, Integration of activating and inhibitory receptor signaling by regulated Vav1 phosphorylation (pdf)
12:00-14:30 Lunch
Dining Hall is open 11:30 AM - 1:30 PM for lunch
14:30-18:00 Session VII - Anton Zilman (chair)
14:30-15:00 Rob Phillips, California Institute of Technology, A single-molecule view of biological action at a distance
15:00-15:20 Contributed Talk: Alexander Y. Mitrophanov, Washington University School of Medicine, Quantitative properties of post-translationally regulated genetic circuits. (pdf)
15:20-15:50 Timothy C. Elston, University of North Carolina, Yeast chemotrophic growth: an attractive model system
15:50-16:20 Coffee Break
16:20-16:40 Contributed Talk: Brian Munsky, Los Alamos National Laboratory,, Stochastic model validation for the Pap (pili) epigenetic switch (pdf)
16:40-17:10 Leonid A. Mirny, Massachusetts Institute of Technology, How do proteins find and bind their sites on DNA?
17:10-17:30 Contributed Talk: William S. Ryu, University of Toronto, Thermal impulse response and temperature preference of Escherichia coli (pdf)
17:30-18:00 Charles D. Little, University of Kansas Medical Center, Cellular v. tissue motion during embryogenesis
18:00-18:30 Break
18:30-20:30 Closing Banquet (Dining Hall)
18:30-18:40 Farewell, Organizers
18:40-19:40 Dinner
19:40-19:45 Introduction of Dr. Levine, Michael A. Savageau, Ulam Visiting Scholar, Center for Nonlinear Studies, Los Alamos National Laboratory
19:45-20:30 Michael Levine, University of California, Berkeley, Dynamic gene circuits control Drosophila embryogenesis

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