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The Sixth q-bio Conference Detailed Program

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Wednesday, August 8, 2012

13:00 - 19:00 Tutorial Sessions

13:00 - 16:00 A systems guide to chemical-biological interactions, Tudor I. Oprea, University of New Mexico School of Medicine
13:00 - 16:00 Rule-based modeling with BioNetGen, James R. Faeder, University of Pittsburgh School of Medicine
13:00 - 16:00 Using gene expression noise to understand gene regulation, Brian Munsky, Los Alamos National Laboratory, and Gregor Neuert, MIT
13:00 - 15:00 Partial least squares regression (PLSR) for the discovery of new biology, Gerard J. Ostheimer, US Department of Agriculture,
16:00 - 19:00 PySB, a programming environment to generate algorithmic representations of biological systems, Carlos F. Lopez, Harvard Medical School
16:00 - 19:00 Using Smoldyn to model cell biology with spatial and stochastic detail, Steven S. Andrews, Fred Hutchinson Cancer Research Center
16:00 - 19:00 Single-molecule studies of biomolecular function, Peter Goodwin and Jaemyeong Jung, Los Alamos National Laboratory
16:00 - 19:00 Information processing in cell biology, Ilya Nemenman, Emory University

19:00 - 21:00 Banquet, St. John's Cafeteria

19:00 - 19:05 Introduction by Organizers, Michael Wall, 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 Sixth q-bio Summer School, Brian Munsky, Los Alamos National Laboratory
19:20 - 20:00 Dinner
20:00 - 20:05 Banquet Speaker Introduction, Gnana Gnanakaran, Los Alamos National Laboratory
20:05 - 21:00 Opening Banquet Talk, The allergic reaction -- some triumphs, some failures, and some cell signaling, Byron Goldstein, Los Alamos National Laboratory

Thursday, August 9, 2012

7:30 - 9:00 Breakfast, St. John's Cafeteria

9:00 - 12:35 Session I, Great Hall

Chair: Brian Munsky, Los Alamos National Laboratory
9:00 - 9:30 Invited Talk 1, Models of moving cell morphologies, Herbert Levine, Rice University
9:30 - 9:50 Contributed Talk 1, Optimal resource allocation or greed, what determines a winning strategy for nutrient sensing?, Andrea Weisse, University of Edinburgh
9:50 - 10:10 Contributed Talk 2, Design rules for bacterial enhancers, Roee Amit, Technion - Israel Institute of Technology
10:10 - 10:40 Invited Talk 2, Developmental regulation and cell lineage control in sensory epithelia, Anne Calof, University of California, Irvine
10:40 - 11:05 Coffee Break
11:05 - 11:25 Poster Spotlights I
Poster Spotlight 1, Multiplicative mutations, sparseness and modularity in biological systems, Tamar Friedlander, Weizmann Institute of Science
Poster Spotlight 2, Network architectures compatible with the nonmonotonic dynamics of central metabolism genes under hypoxic stress in M. tuberculosis, Baris Hancioglu, Rice University
Poster Spotlight 3, Statistical analysis of stochastic biochemical signaling: inference, information processing and experimental design, Michal Komorowski, Polish Academy of Sciences
Poster Spotlight 4, Orchestrating chromosome segregation using the Par system, Saeed Saberi, Simon Fraiser University
Poster Spotlight 5, The effect of physical and mechanical properties of aligned collagen on breast cancer cell migration, Kristin Riching, University of Wisconsin at Madison
11:25 - 11:55 Invited Talk 3, Quantitative analysis of growth arrest variability in bacteria, Nathalie Balaban, Hebrew Univesrity Jerusalem
11:55 - 12:15 Contributed Talk 3, Disentangling the sources of species-specific gene expression patterns in drosophila embryos, Zeba Wunderlich, Harvard Medical School
12:15 - 12:35 Contributed Talk 4, Immune repertoire profiling by high-throughput sequencing, Jiankui He, South University of Science and Technology of China

12:35 - 14:30 Lunch, Great Hall

13:30 - 14:30 How can an NIH program director help your career. An informal Q&A session with Jerry Li, National Cancer Institute

14:30 - 18:20 Session II, Great Hall

Chair: Yi Jiang, Georgia State University
14:30 - 14:35 Introduction of Pioneer Speaker, Ilya Nemenman, Emory University
14:35 - 15:15 Pioneer Talk, The population and evolutionary dynamics of adaptive immunity in bacteria: CRISPR and too much fun, Bruce Levin, Emory University
15:15 - 15:35 Contributed Talk 5, Single-cell measurements imply that replication licenses division during chemostatic growth in E. coli, Enrique Balleza, Harvard University
15:35 - 15:55 Contributed Talk 6, Spatio-temporal measurements and modeling of genetic expression, Douglas Shepherd, Los Alamos National Lab
15:55 - 16:25 Invited Talk 4, The spatial organization of growth factor signaling systems in cells, Philippe Bastiaens, Max Planck Institute, Dortmund
16:25 - 16:55 Coffee Break
16:55 - 17:10 Poster Spotlights II
Poster Spotlight 6, Parameter estimation from live cell siRNA data predicts gene function from dynamics, Samuel Bandara, Stanford University
Poster Spotlight 7, Noise buffering of gene expression by decoys, Anat Burger, UC San Diego
Poster Spotlight 8, Long-noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment, Gregor Neuert, Massachusetts Institute of Technology
Poster Spotlight 9, Network modeling of focal adhesion-invadopodia transitions, Alissa Weaver, Vanderbilt University Medical Center
17:10 - 17:40 Invited Talk 5, Structural and stationary intervention in gene regulatory networks, Edward Dougherty, Texas A&M University
17:40 - 18:00 Contributed Talk 7, Consequences of feedbacks in mammalian signal transduction for cancer therapy, Nils Bluethgen, Charite / Humboldt University Berlin
18:00 - 18:20 Contributed Talk 8, Competing positive and negative feedbacks mediated by PH domain ligand interactions regulate ltk kinase activation kinetics in T cells, Jayajit Das, Nationwide Childrens Hospital and Ohio State University

18:20 - 20:30 Dinner in town (no meal service at St. John's)

20:30 - 23:30 Poster Session I, Junior and Senior Commons Rooms

All posters with the assigned number starting with A (A1--A69) present at this poster session. You should consult the list of posters for this session for your assigned number.

Friday, August 10, 2012

7:30 - 9:00 Breakfast, St. John's Cafeteria

9:00 - 12:25 Session III, Great Hall

Chair: William Hlavacek, Los Alamos National Laboratory
9:00 - 9:20 Contributed Talk 9, Dynamics of cell fate decision-making in Bacillus subtilis, Anna Kuchina, UT Southwestern Medical Center at Dallas
9:20 - 9:40 Contributed Talk 10, Cooperation is favored in expanding populations, Manoshi Datta, Massachusetts Institute of Technology
9:40 - 10:00 Contributed Talk 11, Crossing valleys in multipeaked adaptive landscapes - aided by fluctuations in the environment, Marjon de Vos, AMOLF
10:00 - 10:30 Invited Talk 7, Fluctuations and response in sensory systems, Massimo Vergassola, Pasteur Institute
10:30 - 11:00 Coffee Break
11:00 - 11:15 Poster Spotlights
Poster Spotlight 10, Negative feedback confers mutational robustness in yeast transcription factor Rregulation, Charles Denby, University of California, Berkeley
Poster Spotlight 11, Population dynamics of bacteriophage T7 on heterogeneous Escherichia coli substrates, Wolfram Moebius, Harvard University
Poster Spotlight 12, Disentangling the X chromosome inactivation network, Edda Schulz, Institut Curie
Poster Spotlight 13, Ultrasensitivity in 'anti-zero-order' regimes, Bruno Martins, The University of Edinburgh
11:15 - 11:45 Invited Talk 8, Quantifying the diversity of antibody receptors, Aleksandra Walczak, Ecole Normale Superieur
11:45 - 12:05 Contributed Talk 12, Spatial control principles in cell cycle regulation, Silvia Santos, Stanford University
12:05 - 12:25 Contributed Talk 13, NF-kB mediates inflammation but not survival in individual cells treated with TRAIL, Deborah Flusberg, Harvard Medical School

12:25 - 14:30 Lunch, St. John's Cafeteria

14:30 - 18:10 Session IV, Great Hall

Chair: Gnana Gnanakaran, Los Alamos National Laboratory
14:30 - 15:00 Invited Talk 9, Coping with stress in a synthetic world, Lingchong You, Duke University
15:00 - 15:20 Contributed Talk 14, Stripe formation in bacterial systems with density-suppressed motility, Xiongfei Fu, The University of Hong Kong
15:20 - 15:40 Contributed Talk 15, Spatial reciprocity limits public good diffusion in bacterial colonies growing on a surface, Nicolas Desprat, Ecole Normale Superieure
15:40 - 16:10 Invited Talk 10, Transitions in Darwinian individuality, Paul Rainey, Massey University
16:10 - 16:40 Coffee Break
16:40 - 17:00 Poster Spotlights III
Poster Spotlight 14, Model checking for studying temporal behavior in cell differentiation, Natasa Miskov-Zivanov, University of Pittsburgh
Poster Spotlight 15, Modeling reciprocal altruism and quorum sensing in biofilms, David Bruce Borenstein, Princeton University
Poster Spotlight 16, Hearing the shape of cancer: Spectral graph theory for pathway analysis of gene expression data, Rosemary Braun, Northwestern University
Poster Spotlight 17, Scaling and systems biology for integrating multiple organs-on-a-chip, John Wikswo, Vanderbilt University
17:00 - 17:30 Invited Talk 11, The Matrix: How the mechanics of the environment Informs critical cell decisions, Andre Levchenko, Johns Hopkins University
17:30 - 17:50 Contributed Talk 16, Elucidating multiscale mechanisms of cancer cell reprogramming: Theory and experiment, Jennifer Kasemeier-Kulesa, Stowers Institute for Medical Research
17:50 - 18:10 Contributed Talk 17, Growth bistability from obligatory interactions between antibiotics and antibiotic resistance, Minsu Kim, University of California at San Diego

18:15 - 20:15 Session V, Special Dinner Session, Koi Pond and Great Hall

Chair: Ilya Nemenman, Emory University
18:15 - 19:15 Dinner service
19:15 - 19:20 Special Session Introduction, Ilya Nemenman, Emory University
19:20 - 20:15 Special Session Talk, q-bio Education, David Botstein, Princeton University

20:30 - 23:30 Poster Session II, Junior and Senior Commons Rooms

All posters with the assigned number starting with B (B1--B69) present at this poster session. You should consult the list of posters for this session for your assigned number.

August 11, Saturday

7:30 - 9:00 Breakfast, St. John's Cafeteria

9:00 - 12:40 Session VI, Great Hall

Chair: Michael Wall, Los Alamos National Laboratory
9:00 - 9:30 Invited Talk 12, Enabling life with a molecular toolkit of genes and proteins designed de novo, Michael Hecht, Princeton University
9:30 - 9:50 Contributed Talk 18, A gradient modulated intercellular feedback controlling pattern formation inside intestinal crypts, Kai-Yuan Chen, Cornell University
9:50 - 10:10 Contributed Talk 19, Contact guidance of amoeboid cells via nanotopography, Wolfgang Losert, University of Maryland, College Park
10:10 - 10:40 Invited Talk 13, Porting the auxin signaling pathway to yeast, Eric Klavins, University of Washington
10:40 - 11:10 Coffee Break
11:10 - 11:40 Invited Talk 14, TBA, Michael Yaffe, Massachusetts Institute of Technology
11:40 - 12:00 Contributed Talk 20, Predictive control of an engineered optogenetic signaling pathway in E. coli, Evan Olson, Rice University
12:00 - 12:20 Contributed Talk 21, Mechanism and potential diversity of T-cell receptor rearrangement from sequence repertoires, Anand Murugan, Princeton University
12:20 - 12:40 Contributed Talk 22, Asymmetric segregation of nucleoplasmic factors during yeast closed mitosis, Tatiana T. Marquez-Lago, Okinawa Institute of Science and Technology

12:40 - 14:30 Lunch, St. John's Cafeteria

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

Chair: James Faeder, University of Pittsburgh School of Medicine
14:30 - 15:00 Invited Talk 15, Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway, David Botstein, Princeton University
15:00 - 15:20 Contributed Talk 23, Toggling cell fate by kinase control, Gerard Ostheimer, Unite States Department of Agriculture
15:20 - 15:40 Contributed Talk 24, Computational model for autophagic vesicle dynamics in single cells, Dipak Barua, Los Alamos National Laboratory
15:40 - 16:10 Invited Talk 16, Generation and synchronization of oscillations in synthetic gene networks, Lev Tsimring, University of California, San Diego
16:10 - 16:40 Coffee Break
16:40 - 17:00 Contributed Talk 25, Spatial dynamics of Orai1-STIM1 coupling for calcium entry in antigen-stimulated mast cells, Bridget Wilson, University of New Mexico
17:00 - 17:20 Contributed Talk 26, Mechanisms of chain migration: Theory and experiment, Paul Kulesa, Stowers Institute for Medical Research
17:20 - 17:40 Contributed Talk 27, Adaptive immunity: Why some microbes have it and others don’t, Ariel Weinberger, Harvard
17:40 - 18:30 Break

18:30 - 20:30 Closing Banquet, St. John's Cafeteria

18:30 - 18:35 Farewell, Brian Munsky, Los Alamos National Laboratory
18:35 - 19:30 Dinner
19:30 - 19:35 Banquet Speaker Introduction, William Hlavacek, Los Alamos National Laboratory
19:35 - 20:30 Closing Banquet Talk, Beyond q-bio?, Arthur Lander, University of California, Davis

August 12, Sunday

The day for informal discussions, small group meetings, and exploring Santa Fe and Northern New Mexico.
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