5th q-bio Conference Schedule

  • August 10, 2011
  • 12:00  -  17:00
    Wednesday Tutorials
    17:30  -  20:00
    Opening Banquet
  • August 11, 2011
  • 07:30  -  08:30
    Thursday Breakfast
    08:30  -  12:15
    Thursday Morning: Session I
    12:15  -  14:30
    Thursday Lunch
    14:30  -  18:25
    Thursday Afternoon: Session II
    18:25  -  20:30
    Dinner (no meal service)
    20:30  -  23:30
    Thursday Evening: Poster Session I
  • August 12, 2011
  • 07:30  -  08:30
    Friday Breakfast
    08:30  -  12:15
    Friday Morning: Session III
    12:15  -  14:30
    Friday Lunch
    14:30  -  18:15
    Friday Afternoon: Session IV
    18:15  -  18:30
    18:30  -  20:00
    Friday Dinner (service at Koi pond)
    19:00  -  20:00
    Friday Evening: Session V (special session on the social aspects of science)
    20:00  -  23:30
    Friday Evening: Poster Session II
  • August 13, 2011
  • 07:30  -  09:10
    Saturday Breakfast
    09:10  -  12:30
    Saturday Morning: Session VI
    12:30  -  14:30
    Saturday Lunch
    14:30  -  18:10
    Saturday Afternoon: Session VII
    18:10  -  18:30
    18:30  -  20:30
    Closing Banquet
  • August 14, 2011
  • 09:00  -  17:00
    Sunday Satellite: Second Workshop on Rule-based Modeling of Biochemical Systems

Detailed Program:

Wednesday August 10, 2011
  12:00-17:00 Tutorial Session, Classrooms (check registration desk)
  12:00-14:00 Steven Gross, University of California, Irvine, From single motors to ensemble function: What is important for how motors work together?
  12:00-13:30 James Faeder, University of Pittsburgh School of Medicine, Rule-based modeling with BioNetGen
  14:00-17:00 James Glazier, Indiana University, Developing multi-cell developmental and biomedical simulations using CompuCell3D
  14:00-17:00 Ilya Nemenman , Emory University, Information processing in cell biology
  14:00-17:00 Tudor Oprea, Gergely Zahoransky-Kohalmi, and Jeremy Yang, University of New Mexico, Network-based analyses of drugs, targets, and clinical outcomes
  14:00-17:00 Avi Ma'ayan, Mount Sinai School of Medicine, Icahn Medical Institute, Tutorial: Network analysis and gene-list enrichment analysis in systems biology
  15:00-17:00 Brian Munsky and Gregor Neuert, Los Alamos National Laboratory and MIT, Identifying stochastic models using flow cytometry and fluorescence microscopy
  17:30-20:00 Opening Banquet, Great Hall
  17:30-17:45 Welcome Comments from Organizers and LANL Administration
  17:45-17:50 Summer School Recap, Brian Munsky, Los Alamos National Laboratory
  17:50-19:00 Dinner
  19:00-19:05 Banquet Speaker Introduction, Ilya Nemenman , Emory University
  19:05-20:00 Opening Banquet Talk, Dennis Bray, University of Cambridge, Protein Computations and the Origins of Behavior
Thursday August 11, 2011
  7:30-8:30 Breakfast, Dining Hall (service 7:30-9:30)
  8:30-12:15 Session I, Great Hall, Chair: Yi Jiang, Los Alamos National Laboratory
  8:30-9:00 Uri Alon, Weizmann Institute, Design principles of Biological Circuits
  9:00-9:20 Tom Shimizu, FOM Institute AMOLF, Response rescaling in bacterial chemotaxis
  9:20-9:40 Sriram Chandrasekaran, University of Illinois, Urbana-Champaign, Brain Transcriptional Regulatory Network Quantitatively Predicts Behavior-Specific Gene Expression
  9:40-10:00 Gregor Neuert, Massachusetts Institute of Technology, Systematic Identification of Signal-Activated Stochastic Gene Regulation
  10:00-10:30 Coffee Break
  10:30-10:45 Poster Spotlights I
    Emily Capra, Massachusetts Institute of Technology, Evolution of two-component signaling systems
    Xianrui Cheng, Duke University, Autonomous Boolean models reveal timing constraints on embryonic developmental pattern formation
    Lily Chylek, Cornell University, Interaction libraries for rule-based modeling
  10:45-11:15 Pieter Rein ten Wolde, FOM Institute AMOLF, Single-cell ultrasensitivity and stochasticity give rise to bimodal response on the population level
  11:15-11:35 Fang Huang, University of New Mexico, Fast, simultaneous multiple-emitter fitting for single molecule super-resolution imaging
  11:35-11:55 Lei Dai, Massachusetts Institute of Technology, Experimental Observation of Early Warning Signals for Approaching Population Collapse
  11:55-12:15 Xiling Shen , Cornell University, Asymmetric Cell Fate Decisions in Colon Cancer Stem Cells
  12:15-14:30 Lunch, Dining Hall (service 11:30-13:30)
  14:30-18:25 Session II, Great Hall, Chair: James Fader, University of Pittsburgh School of Medicine
  14:30-15:10 Pioneer Talk, Nadrian Seeman, New York University, DNA: Not Merely the Secret of Life
  15:10-15:30 Oleg Igoshin, Rice University, Self-organization mechanisms in Myxococcus xanthus swarms
  15:30-15:50 Robert Egbert , University of Washington, Tuning Gene Networks with Simple Sequence Repeats
  15:50-16:10 Kevin Wood, Harvard University, Using Maximum Entropy to Decode the Multi-drug Response in Bacteria
  16:10-16:40 Coffee Break
  16:40-16:55 Poster Spotlights II
    John Kang, Carnegie Mellon University, Coarse-grained Modeling of Actin Cytoskeletal Alignment to Mechanical Stimulation
    Eric Batchelor, Harvard Medical School , Stimulus-dependent dynamics of p53 in single cells
    Eugene Yurtsev, Massachusetts Institute of Technology, Microbial Cheating Limits the Evolution of Antibiotic Resistance
  16:55-17:25 Diane Lidke, University of New Mexico, Measuring Membrane Receptor Interactions Using Single Quantum Dot Tracking
  17:25-17:45 Eric Deeds, The University of Kansas, Optimizing ring assembly: the strength of weak bonds
  17:45-18:05 Can Guven, University of Maryland, Stability Analysis of a Model for Collective Migration of Dictyostelium Discoideum
  18:05-18:25 Maciej Dobrzynski, Systems Biology Ireland, University College Dublin, Single-cell ultrasensitivity and stochasticity give rise to bimodal response on the population level
  18:25-20:30 Dinner in town , (no meal service at St. John's)
  20:30-23:30 Poster Session I (q-Bio-Poster-Set-1a, q-Bio-Poster-Set-1b)
Friday August 12, 2011
  7:30-8:30 Breakfast, Dining Hall (service 7:30-9:30)
  8:30-12:15 Session III, Great Hall, Chair: William Hlavacek, Los Alamos National Laboratory and Translational Genomics Research Institute
  8:30-9:00 Reka Albert, Pennsylvania State University, Discrete dynamic modeling of signal transduction networks
  9:00-9:20 David Klinke , West Virginia University, Quantifying cross-talk among Interferon-γ, Interleukin-12 and Tumor Necrosis Factor signaling pathways within a TH1 cell model: A model-based inference approach
  9:20-9:40 Mohammad Fallahi-Sichani, University of Michigan, The dynamics of TNF signaling control tuberculosis granuloma formation
  9:40-10:00 Huilei Xu, Mount Sinai School of Medicine, Functional Atlas of Mouse Embryonic Stem Cells Pluripotency and Early Differentiation
  10:00-10:30 Coffee Break
  10:30-10:45 Poster Spotlights III
    Jakub Otwinowski, Emory University, Speeding up evolutionary search by small fitness fluctuations
    Christian Ray, University of Texas M. D. Anderson Cancer Center, Amelioration of ultrasensitive biochemical switches in bacteria
    John Sekar, University of Pittsburgh, Experimental Design in Rule-Based Models
  10:45-11:15 Tobias Meyer, Stanford University, A two dimensional Akt-Erk signaling code for NGF-triggered differentiation and cell number expansion
  11:15-11:35 Edward Stites, Translational Genomics Research Institute, Promiscuity quantitatively and qualitatively impacts early growth factor receptor signaling
  11:35-11:55 Raymond Cheong, Johns Hopkins University, Advantages and limitations of network-based information processing in biological signaling systems
  11:55-12:15 Christopher Zopf, Massachusetts Institute of Technology, Single promoters as regulatory network motifs
  12:15-14:30 Lunch, Dining Hall (service 11:30-13:30)
  14:30-18:15 Session IV, Great Hall, Chair: Gnana Gnanakaran, Los Alamos National Laboratory
  14:30-15:00 Alan Perelson, Los Alamos National Laboratory, Multiscale Modeling of Hepatitis C Virus Infection
  15:00-15:20 Cheemeng Tan , Carnegie Mellon University, The inoculum effect and band-pass bacterial response to periodic antibiotic treatment
  15:20-15:40 Ni Ji, Massachusetts Institute of Technology, _Genetic redundancy in the Wnt pathway promotes robust control of neuronal migration through interlocked feedback loops
  15:40-16:00 Karina Mazzitello, Universidad Nacional de Mar del Plata, Modeling Morphology Dynamics of Retinal Pigment Epithelium
  16:00-16:30 Coffee Break
  16:30-16:45 Poster Spotlights IV
    Rui Zhen Tan, Massachusetts Institute of Technology, Different roles of Wnt ligands and receptors in regulating C.elegans' cell divisions
    Karen Tkach, Memorial Sloan Kettering Cancer Center, Regulation of T cell Antigen Dose-Dependent IL-2 Production via Population Dynamics
    Cathy McKinney, Stowers Institute for Medical Research, Semi-Automated Analysis of Proliferation Dynamics of Human Metastatic Melanoma
  16:45-17:15 Michael Laub, Massachusetts Institute of Technology and Howard Hughes Medical Institute, Specificity and Evolution of Bacterial Signaling Pathways
  17:15-17:35 Howard Salis, Pennsylvania State University, Automated Design of Synthetic Bacterial Small RNAs
  17:35-17:55 Mark Maienschein-Cline, University of Chicago, Identification of transcription factor targets by analysis of high-throughput data
  17:55-18:15 Veronika Zarnitsyna, Georgia Institute of Technology, Kinetics of molecular interactions across the T cell – APC junction
  18:15-18:30 Break
  18:30-20:00 Dinner (service), Koi Pond
  19:00-20:00 Session V, Koi Pond, Chair: Michael Wall, Los Alamos National Laboratory
  19:00-19:05 Introduction on the Social Aspects of Science
  19:05-20:00 Guitar Session: Love and Fear in the Lab, Uri Alon, Weizmann Institute
  20:00-23:00 Poster Session II (q-Bio-Poster-Set-2a, q-Bio-Poster-Set-2b)
Saturday August 13, 2011
  7:30-9:10 Breakfast, Dining Hall (service 7:30-9:30)
  9:10-12:30 Session VI, Great Hall, Chair: Brian Munsky, Los Alamos National Laboratory
  9:10-9:40 Nicole King, University of California, Berkeley, The origin of animal multicellularity
  9:40-10:00 Evgeni Nikolaev, Rutgers, The State University of New Jersey, Mathematical Modeling Describes a Novel Bistable Mechanism of Lipid Body Formation in Macrophages Infected with M. tuberculosis
  10:00-10:20 Rebecca McLennan, Stowers Institute for Medical Research, Elucidating multiscale mechanisms of neural crest migration
  10:20-10:50 Wallace Marshall, University of California, San Francisco, Biological Noise at the level of Cellular Structure
  10:50-11:20 Coffee Break
  11:20-11:50 Stas Shvartsman, Princeton University, Multiscale studies of embryonic development: experiments and theory
  11:50-12:10 Stephen Helms, University of Texas Southwestern Medical Center, A Tandem PDZ Domain Redox Switch in InaD
  12:10-12:30 Domitilla Del Vecchio, Massachusetts Institute of Technology, The Impact of Retroactivity on the Signal Processing of Transduction Networks
  12:30-14:30 Lunch, Dining Hall (service 11:30-13:30)
  14:30-18:10 Session VII, Great Hall, Chair: Ilya Nemenman, Emory University
  14:30-15:00 Alexander Hoffmann, University of California, San Diego, Parsimonious Gene Regulatory Network modeling reveals mRNA half-life control of the pathogen-responsive transcriptome
  15:00-15:20 Bernie Daigle, Jr., University of California, Santa Barbara, Accelerated Maximum Likelihood Estimation for Stochastic Biochemical Systems
  15:20-15:40 Alistair Boettiger, University of California, Berkeley, No Compromise: Single molecule imaging reveal mechanisms for speed and precision in developmental gene expression
  15:40-16:10 Vittorio Cristini, University of New Mexico, Tumor Modeling
  16:10-16:40 Coffee Break
  16:40-17:10 Michael Deem, Rice University, Heterogeneous Diversity of Spacers within CRISPR
  17:10-17:30 Qiong Yang, Stanford University, Switch-like negative feedback promotes clock-like mitotic oscillation
  17:30-17:50 Alexandra Jilkine, University of Arizona, A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules
  17:50-18:10 Wan-Chen Lin, University of California, Berkeley, Spatial organization in cell membranes
  18:10-18:30 Break
  18:30-20:30 Closing Banquet, Dining Hall
  18:30-18:35 Farewell, Michael Wall, Los Alamos National Laboratory
  18:35-19:30 Dinner
  19:30-19:35 Banquet Speaker Introduction, William Hlavacek, Los Alamos National Laboratory and Translational Genomics Research Institute
  19:35-20:30 Closing Banquet Talk, Peter Sorger, Harvard Medical School, Measuring and Modeling Cell Decision Processes
Sunday August 14, 2011
  9:00-17:00 Sunday Satellite: Second workshop on rule-based modeling of biochemical systems


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