The Fourth q-bio Conference on Cellular Information Processing

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The Fourth q-bio Conference on Cellular Information Processing is scheduled for August 11-14, 2010. The conference is sponsored by the National Institute of General Medical Sciences, the New Mexico Center for Systems Biology, and the Center for Nonlinear Studies at Los Alamos National Laboratory.

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

Contents

Dates and Venue

Important announcements

Participants

Affiliated pre-conference events

The conference will be preceeded by The Fourth q-bio Summer School on Cellular Information Processing in Los Alamos, July 26-August 10, 2010. The summer school is sponsored by the New Mexico Center for Systems Biology, the Center for Nonlinear Studies at Los Alamos National Laboratory, and the Los Alamos Institute for Advanced Studies.

Program

Wednesday, August 11

12:00-17:00 Tutorials
  • Classroom I
12:00-13:30 Yi Jiang, Los Alamos National Laboratory, Multiscale Modeling Starting from Cell-based Models
13:45-15:15 James R. Faeder, University of Pittsburgh School of Medicine, Rule-based Modeling with BioNetGen
15:30-17:00 Michael Sneddon, Yale University, Simulating and Coarse-graining Complex Biological Systems with NFsim
  • Classroom II
12:00-13:30 Ramit Mehr, Bar-Ilan University, The Immunomics of Lymphocyte Repertoires (a Tasting Menu)
13:45-15:15 Brian Munsky, Los Alamos National Laboratory, Analyzing and Identifying Stochastic Models Using Flow Cytometry and Fluorescence Microscopy
15:30-17:00 Ramit Mehr (discussion leader), Bar-Ilan University, Balancing a career in science with raising a family
17:00-17:30 Reception
17:45-19:50 Opening Banquet (Great Hall)
17:45-17:50 Welcome, Organizers
17:50-18:00 Welcome, Robert Ecke, Director, Center for Nonlinear Studies, Los Alamos National Laboratory
18:00-19:00 Dinner
19:00-19:05 Banquet Speaker Introduction, William Hlavacek, Los Alamos National Laboratory
19:05-19:50 Michael A. Savageau, University of California, Davis, Searching for System Design Principles

Thursday, Aug 12, 2010

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
08:30-12:10 Session I, Session Chair: Ilya Nemenman, Emory University
08:30-09:00 Bonnnie L. Bassler, Princeton University, Information Processing in Quorum Sensing Circuits
09:00-09:20 Contributed Talk: Gabor Balazsi, The University of Texas MD Anderson Cancer Center, Population-level control of gene expression
09:20-09:40 Contributed Talk: Naama Brenner, Technion, Israel, Adaptive Response and Background Signal Compensation
09:40-10:10 Christopher A. Voigt, University of California, San Francisco, Quantitative Methods for Genetic Programming
10:10-10:35 Coffee Break
10:35-10:50 Poster Spotlights
Jeffrey Enders, Vanderbilt University, Characterizing the Saccharomyces cerevisiae respiratory oscillation exometabolome by ion mobility-mass spectrometry
Ambhi Ganesan, Johns Hopkins University, PKA is a control node in a Ca2+-dependent oscillatory circuit in pancreatic beta cells
Sachin Goyal, Emory University, Determination of the number of proteins bound non-specifically to DNA
Yuval Hart, Weizmann Institute, Robust Control in the Nitrogen Assimilation System of E.coli
10:50-11:10 Contributed Talk: Ryan N. Gutenkunst, Los Alamos National Laboratory, Inferring the demographic history of multiple populations from genomic polymorphism data
11:10-11:30 Contributed Talk: Michael Fero, Stanford University, Automation, Computation and the Single Cell: Illuminating Complete Protein Localization Networks
11:30-11:50 Contributed Talk: Paul Francois, Rockefeller University, Predicting Embryonic Patterning using Mutual Entropy Fitness and in silico Evolution
11:50-12:20 Jan Liphardt, University of California, Berkeley, Infinite Regression and Biological Function
12:20-14:30 Lunch
Dining Hall is open 11:30 AM -1:30 PM for lunch
14:30-18:10 Session II, Session Chair: James Faeder, University of Pittsburgh, School of Medicine
14:30-15:00 Leor S. Weinberger, University of California, San Diego, Halting Infectious-Disease Spread with Engineered Transmissible Therapies
15:00-15:20 Contributed Talk: Jaline Gerardin, University of California, San Francisco, Engineering circuits for temporal control
15:20-15:40 Contributed Talk: Alex Groisman, University of California, San Diego, Generation and applications of microfluidic gradients
15:40-16:10 Jehoshua Bruck, California Institute of Technology, Random Ideas about Biological Networks
16:10-16:35 Coffee Break
16:35-16:50 Poster Spotlights II
Jean Hausser, Basel University, Timing matters: Towards a kinetic model of miRNA-mediated gene silencing
Jintao Liu, University of Pittsburgh, Variable Time-Delay to Commitment is the Major Source of Heterogeneity in Bacterial Spore Germination Kinetic
Tetsuya Kobayashi, University of Tokyo, Dynamic Decision Making by Intracellular Kinetics
Savas Tay, Stanford University, Uncorrelated transcription factor dynamics in sister cells
16:50-17:10 Contributed Talk: Jason Haugh, North Carolina State University, Dynamic Regulation of Growth Factor Signaling Networks
17:10-17:30 Contributed Talk: Melissa Kemp, Georgia Institute of Technology, Regulation of the IL-4 cytokine signaling network is distributed via multiple redox-sensitive regulatory mechanisms
17:30-18:00 Thierry Emonet, Yale University, Signaling noise coordinates multiple flagella to enhance bacterial foraging with minimal cost to chemotactic response
18:00-20:30 Dinner (no cafeteria service)
20:30-23:30 Poster Session 1
Drinks and snacks will be served

Friday, Aug 13, 2010

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
08:30-12:00 Session III, Session Chair: William Hlavacek, LANL
08:30-09:00 Stephen R. Quake, Stanford University, Precision Measurement in Biology
09:00-09:20 Contributed Talk: Anat Burger, University of California, San Diego, Abduction and asylum in the lives of transcription factors
09:20-09:40 Contributed Talk: Paul Kulesa, Stowers Institute for Medical Research, Reprogramming multipotent tumor cells with embryonic microenvironments
09:40-10:10 Galit Lahav, Harvard Medical School, Always on Guard: Spontaneous Bursts of p53 in Cycling Cells
10:10-10:35 Coffee Break
10:35-10:50 Poster Spotlights III
Jacob Stewart-Ornstein, University of California, San Francisco, Noise in Gene Expression Reveals Cellular Pathways
Shankar Mukherji, MIT, MicroRNAs generate gene expression thresholds with ultrasensitive transitions
Tatjana Petrov, EPFL, Stochastic Semantics of Rule-based Models
William Pontius, Yale University, Behavioral variability in the bacterial chemotaxis system arising from component localization
10:50-11:10 Contributed Talk: Yihan Lin, University of Chicago, Phase Response of the Cell Cycles to Perturbations
11:10-11:30 Contributed Talk: Narendra Maheshri, MIT, Regulatory Role of Tandem Repeats
11:30-11:50 Contributed Talk: Debora Marks, Harvard Medical School, Saturation and competition drive siRNA and microRNA activity: It's more than the binding sites
11:50-12:20 Victor Sourjik, Heidelberg University, Robustness of signalling in bacterial chemotaxis
12:20-14:30 Lunch
Dining Hall is open 11:30 AM - 1:30 PM for lunch
14:30-16:15 Session IV, Session Chair: Michael Wall, LANL
14:30-15:00 Michael B. Elowitz, California Institute of Technology, Signaling Dynamics at the Single-Cell Level
15:00-15:20 Contributed Talk: Bruno Martins, University of Edinburgh, Functional Trade-offs in Allosteric Sensing
15:20-15:40 Contributed Talk: Yi Jiang, Los Alamos National Laboratory, Cell order in bacterial swarms arises from reversals of moving direction
15:40-16:00 Contributed Talk: Anurag Sethi, Los Alamos National Lab, Interplay Between Reaction Stoichiometry and Effective Concentration: A Structure-based Synergetic Study on Grb2:Sos1 Complex
16:00-16:25 Coffee Break
16:25-16:40 Poster Spotlights IV
Barak Peleg, Weizmann Institute, Up and Down: membrane waves driven by curved activators of actin polymerization
Mei-Lyn Ong, MIT, Genetic control of robustness and tunability in the yeast osmosensing signaling pathway
Mark Maienschein-Cline, University of Chicago, Integration of high-throughput DNA binding and gene expression data to understand effector B cell fate choice
Julia Tsitron, Rutgers, The State University of New Jersey, A Biophysical Model of Chemical Sensing
16:40-17:00 Contributed Talk: Natasa Miskov-Zivanov, University of Pittsburgh School of Medicine, Modeling of Peripheral T Cell Differentiation
17:00-17:20 Contributed Talk: Hyun Youk, MIT, Pluripotency signatures in single embryonic stem cells
17:20-17:50 Boris I. Shraiman, University of California, Santa Barbara, Recombination, genetic interactions and the rate of adaptation in large populations
17:50-20:30 Dinner (no cafeteria service)
20:30-23:30 Poster Session 2
Drinks and snacks will be served

Saturday, Aug 14, 2010

07:30-08:30 Breakfast
Dining Hall is open 7:30-9:30 AM for breakfast
08:30-12:00 Session V, Session Chair: Yi Jiang, LANL
08:30-09:00 John J. Tyson, Virginia Polytechnic and State University, Stochastic Models of Cell Cycle Regulation in Eukaryotes
09:00-09:20 Contributed Talk: Octavio Mondragon-Palomino, University of California, San Diego, Entrainment of bacterial synthetic clocks
09:20-09:40 Contributed Talk: Philippe Nghe, AMOLF, Amsterdam, Evolution of phenotypic plasticity in a synthetic regulatory network
09:40-10:10 Ned S. Wingreen, Princeton University, Why are chemotaxis receptors clustered but other receptors aren't?
10:10-10:35 Coffee Break
10:35-11:05 Christopher V. Rao, University of Illinois, Urbana-Champaign, Counting and control in bacterial motility
11:05-11:25 Contributed Talk: Justin Kinney, CSHL, Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
11:25-11:45 Contributed Talk: Khalid Salaita, Emory University, Spatio-Mechanical Inputs Alter ErbB Receptor Functions
11:45-12:15 Jan M. Skotheim, Stanford University, Cell cycle commitment
12:15-14:30 Lunch
Dining Hall is open 11:30 AM - 1:30 PM for lunch
14:30-18:00 Session VI, Session Chair: Anton Zilman, LANL
14:30-15:00 Hana El-Samad, University of California, San Francisco, A Chaperone Network Modulates the Homeostatic Regulation of the Unfolded Protein Response
15:00-15:20 Contributed Talk: Silvia Santos, Stanford University, Spatial positive feedback at the onset of mitosis
15:20-15:40 Contributed Talk: Alex Sigal, California Institute of Technology, Direct cell to cell transmission of HIV confers resistance to therapy and may produce a virus reservoir
15:40-16:10 John P. Wikswo, Vanderbilt University, The Robot Scientist or: How I learned to stop worrying and love automated model inference
16:10-16:35 Coffee Break
16:35-17:05 Grégoire Altan-Bonnet, Memorial Sloan-Kettering Cancer Research Center, Signaling heterogeneity and feedback regulation for the cytokine IL-2 enforces self/non-self discrimination in the immune system
17:05-17:25 Contributed Talk: Arvind Subramaniam, Harvard University, Synonymous codon usage determines sensitivity of gene expression to amino acid starvation
17:25-17:45 Contributed Talk: Xiaojing Yang, University of California, San Francisco, Robust switch-like destruction of the CDK inhibitor Sic1 is ensured by a double negative feedback loop
17:45-18:15 Arthur D. Lander, University of California, Irvine, Constraints, objectives and tradeoffs in morphogen-mediated patterning
18:15-18:30 Break
18:30-20:30 Closing Banquet (Dining Hall)
18:30-18:40 Farewell, Organizers
18:40-19:40 Dinner
19:40-19:45 Banquet Speaker Introduction
19:45-20:30 James E. Ferrell Jr., Stanford University, Dissecting the mitotic oscillator



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