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2013 schedule

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Wednesday, August 7, 2013

13:00 - 19:00 Tutorial Sessions

13:00 - 16:00 Senior Common Room, Knowledge Management for Translational Informatics Using the CARLSBAD Platform, Gergely Zahoranszky-Kohalmi
13:00 - 16:00 Junior Common Room, Partial Least Squares Regression for the Discovery of New Biology, Gerald Ostheimer
13:00 - 16:00 Great Hall, Rule-Based Modeling with BioNetGen and RuleBender, James R. Faeder
16:00 - 19:00 Senior Common Room, PySB, a programming environment to generate algorithmic representations of biological systems, Carlos F. Lopez
16:00 - 19:00 Great Hall, Information processing in biological systems, Ilya Nemenman
16:00 - 19:00 Junior Common Room, Modeling spatial effects in carcinogenesis: Stochastic and deterministic reaction-diffusion, Marek Kimmel

19:00 - 21:00 Banquet, Dining Hall

19:00 - 19:05 Introduction by Organizers, Gnana Gnanakaran, Los Alamos National Laboratory
19:05 - 19:15 Welcome, Robert Ecke, Director, Center for Nonlinear Studies, Los Alamos National Laboratory
19:15 - 19:20 The Seventh q-bio Summer School, Brian Munsky, Los Alamos National Laboratory
19:20 - 20:00 Dinner
20:00 - 20:05 Banquet Speaker Introduction, James Faeder, University of Pittsburgh Medical School
20:05 - 21:00 Opening Banquet Talk, Cellular heterogeneity: what do differences tell us? Steven Altschuler, UT Southwestern Medical Center

Thursday, August 8, 2013

7:30 - 9:00 Breakfast, Dining Hall

9:00 - 12:10 Session I, Great Hall

Chair: James Faeder, University of Pittsburgh Medical School
9:00 - 9:30 Invited Talk 2, Microdevices for Advancing Preclinical and Clinical Research, Nancy Albritton, University of North Carolina, Chapel Hill
9:30 - 9:50 Contributed Talk 1, Epigenetic landscapes provide insight into cellular programming, Alex Lang, Boston University
9:50 - 10:10 Contributed Talk 2, Control of the fraction of differentiating mammalian cells by noise in the signaling network architecture, Mary Teruel, Stanford University
10:10 - 10:45 Coffee Break
10:45 - 11:00 Poster Spotlights I
Poster Spotlight 1, Intracellular transport of insulin granules is a subordinated random walk, Ali Tabei, University of Chicago
Poster Spotlight 2, Comparative Analysis of Metabolic Robustness: E. coli and Synechocystis, Ashok Prasad, Colorado State University
Poster Spotlight 3, Enzyme displacement reactions for programmable molecular logic, Carl Brown III, University of New Mexico
11:00 - 11:30 Invited Talk 3, Stochastic simulations of cellular processes: From single cells to colonies, Zaida Luthey-Schulten, University of Illinois, Urbana-Champaign
11:30 - 11:50 Contributed Talk 3, Heterogeneous Differentiation Patterns of Individual CD8+ T Cells, Rob De Boer, Utrecht University
11:50 - 12:10 Contributed Talk 4, Chewing on biology, one bit at a time -- high throughput assays at single-cell resolution using Drop-Based Microfluidics reveal novel variations in heterogeneous populations, Assaf Rotem, Harvard University

12:10 - 14:30 Lunch, Dining Hall

14:30 - 17:35 Session II, Great Hall

Chair: Yi Jiang, Georgia State University
14:30 - 14:35 Introduction of Pioneer Speaker, Ilya Nemenman, Emory University
14:35 - 15:20 Pioneer Talk, Navigating the cellular landscape with new optical probes, imaging strategies and technical innovations, Jennifer Lippincott-Schwartz, National Institutes of Health
15:20 - 15:40 Contributed Talk 5, Information flow in the plasma membrane, Benjamin Machta, Princeton University
15:40 - 16:00 Contributed Talk 6, Modeling Extracellular Matrix in Breast Cancer, Byoungkoo Lee, Georgia State University
16:00 - 16:30 Coffee Break
16:30 - 16:45 Poster Spotlights II
Poster Spotlight 4, Expansion of cell death models to understand the balance between necrosis and apoptosis, Carlos Lopez, Vanderbilt University
Poster Spotlight 5, A phase diagram of regulatory strategies, David Sivak, University of California, San Francisco
Poster Spotlight 6, Emergence of cellular aging from gene networks, Hong Qin, Spellman College
16:45 - 17:15 Invited Talk 5, The Evolutionary "Design" of Proteins, Rama Ranganathan, University of Texas Southwestern Medical Center at Dallas
17:15 - 17:35 Contributed Talk 7, Metabolism Drives Distinct Cellular Growth Phases, Christian Ray, M.D. Anderson Cancer Center

18:20 - 20:00 Special Session - ImprovScience with Raquell Holmes

Improvisation for Q-bio

20:00 - 23:00 Poster Session I

All posters with the assigned number starting with A (A1 - A55) present at this poster session. You should consult the list of posters for this session for your assigned number.
Snacks and drinks served.

Friday, August 9, 2013

7:30 - 9:00 Breakfast, Dining Hall

9:00 - 12:10 Session III, Great Hall

Chair: William Hlavacek, Los Alamos National Laboratory
9:00 - 9:30 Invited Talk 6, Reverse engineering neutrophil polarity network, Lani Wu, University of Texas Southwestern Medical Center at Dallas
9:30 - 9:50 Contributed Talk 8, The evolution of crosstalk in signaling networks, Eric Deeds, University of Kansas
9:50 - 10:10 Contributed Talk 9, Fold-change detection in a social amoeba and cell-cell signaling robust to variations in cell density, Keita Kamino, University of Tokyo
10:10 - 10:40 Coffee Break
10:40 - 11:00 Poster Spotlights III
Poster Spotlight 7, Systems Biology of Epidemiology: From Genes to Environment, Juan Gutierrez, University of Georgia
Poster Spotlight 8, Cell-cycle dominates noisy gene expression, Narendra Maheshri, Massachusetts Institute of Technology
Poster Spotlight 9, Parameter Inference for Virus Capsid Assembly via Simulation-Based Data Fitting, Russell Schwartz, Carnegie Mellon University
Poster Spotlight 10, Mono and Multivalent Ligation of BCR Exhibit Differential Dependence on Syk and Src kinases, Sayak Mukherjee, Ohio State University
11:00 - 11:30 Invited Talk 7, Transient Bimodality Generates an Anticipatory Regulatory Strategy that Enchances Adaptation to Combinatorial Environments, Hana El-Samad, University of California, San Francisco
11:30 - 11:50 Contributed Talk 10, Cells control pattern formation by changing their sensitivity to a morphogen gradient, Jeroen van Zon, FOM Institute AMOLF
11:50 - 12:10 Contributed Talk 11, A Chemical Perturbation Spectroscopy to Elucidate Dynamic Responses of Cellular Networks, Norbert Scherer, University of Chicago

12:10 - 14:30 Lunch, Dining Hall

14:30 - 17:40 Session IV, Great Hall

Chair: Orna Resnekov, MSI
14:30 - 15:00 Invited Talk 8, Models for GTPases in Cell Polarization, Leah Edelstein-Keshet, University of British Columbia
15:00 - 15:20 Contributed Talk 12, Bacterial flagellar motor adaptation and implication for the motor ultrasensitivity, Junhua Yuan, University of Science and Technology China
15:20 - 15:40 Contributed Talk 13, Time Integration of Signal Feedbacks Generates Intensive Scaling of Cytokine Regulation, Karen Tkach, Memorial Sloan Kettering Cancer Center
15:40 - 16:15 Coffee Break
16:15 - 16:30 Poster Spotlights IV
Poster Spotlight 11, Post-transcriptional feedback control of polyamine metabolism in yeast: an integrated modeling and experimental investigation, Svetlana Amirova, East Carolina University
Poster Spotlight 12, Quantitative Sequence Activity Models with a little help from quantum field theory, Vipul Periwal, National Institutes of Health
Poster Spotlight 13, Modeling single-variant bottlenecks in early stages of H. influenzae bacteremia, Xinxian Shao, Emory University
16:30 - 17:00 Invited Talk 9, Programmable cell-free circuitry with genelets, Erik Winfree, California Institute of Technology
17:00 - 17:20 Contributed Talk 14, Bang-bang control of T-cell receptor signaling, Lily Chylek, Cornell University and Los Alamos National Laboratory
17:20 - 17:40 Contributed Talk 15, Why is ERK phosphorylation transient?, Jason Haugh, North Carolina State University

17:40 - 18:00 Break

18:00 - 20:00 Dinner, Koi Pond

19:00 - 20:00 Special Session led by Raquell Holmes on Diversity in q-bio, Koi Pond

The art of building diverse teams for creative science

20:00 - 23:00 Poster Session II

All posters with the assigned number starting with B (B1 - B53) present at this poster session. You should consult the list of posters for this session for your assigned number.
Snacks and drinks served

Saturday, August 10, 2013

7:30 - 9:00 Breakfast, Dining Hall

9:00 - 12:10 Session V, Great Hall

Chair: Anton Zilman, University of Toronto
9:00 - 9:30 Invited Talk 10, Signatures of Mutational Processes in Human Cancer, Ludmil B. Alexandrov, Wellcome Trust Sanger Institute
9:30 - 9:50 Contributed Talk 16, Real-time optogenetic control of intracellular protein concentration in microbial cell cultures, Megan McClean, Princeton University
9:50 - 10:10 Contributed Talk 17, Robust Circadian Timing from a Three-Component Clock, Michael Rust, University of Chicago
10:10 - 10:30 Contributed Talk 18, Mutual coupling between circadian clock and cell cycle in single mammalian cells, Jonathan Beiler, EPFL Institute of Bioengineering
10:30 - 11:00 Coffee Break
11:00 - 11:30 Invited Talk 11, The E. coli chromosome at all growth rates, Suckjoon Jun, University of California, San Diego
11:30 - 11:50 Contributed Talk 19, Single-cell E2F Dynamics Reveal the Control Logic of Cell Cycle Entry, Peng Dong, Duke University
11:50 - 12:10 Contributed Talk 20, A Mutational Path to New Function in a PDZ Domain, Arjun Raman, University of Texas Southwestern Medical Center at Dallas

12:10 - 14:30 Lunch, Dining Hall

14:30 - 17:50 Session VI, Great Hall

Chair: Michael Wall, Los Alamos National Laboratory
14:30 - 15:00 Invited Talk 12, Visualisation of plant morphogenesis, Timothy Rudge, University of Oxford
15:00 - 15:20 Contributed Talk 21, Positive & Negative Regulation of FcεRI Signaling in Mast Cells, Avanika Mahajan, University of New Mexico
15:20 - 15:40 Contributed Talk 22, A Common Behavioral Model Underlies the Motility of a Diverse Set of Nematodes, Stephen Helms, FOM Institute AMOLF
15:40 - 16:00 Contributed Talk 23, Isolated cell behavior drives the evolution of antibiotic resistance, Tanya Artemova, Massachusetts Institute of Technology
16:00 - 16:30 Coffee Break
16:30 - 16:50 Contributed Talk 24, The proliferation-quiescence decision is controlled by a bifurcation in CDK2 activity at mitotic exit, Sabrina Spencer, Stanford University
16:50 - 17:10 Contributed Talk 25, Quantitative mass spectrometry reveals simple patterns of proteome-wide responses to different modes of growth limitation in E. coli, Tony Hui, University of California, San Diego
17:10 - 17:30 Contributed Talk 26, Morphogenesis at criticality?, Dmitry Krotov, Princeton University
17:30 - 17:50 Contributed Talk 27, Impact of Asymmetric Activation and Membrane Landscape on ErbB1 Receptor State, Meghan McCabe, University of New Mexico

17:50 - 18:30 Break

18:30 - 20:30 Closing Banquet, Dining Hall

18:30 - 18:35 Farewell, Gnana Gnanakaran, Los Alamos National Laboratory
18:35 - 19:30 Dinner
19:30 - 19:35 Banquet Speaker Introduction, James Faeder, University of Pittsburgh
19:35 - 20:30 Closing Banquet Talk, The sacred problem of biological specificity illuminated by the profane biophysics of protein degradation, Marc W. Kirschner, Harvard Medical School