2nd q-bio Conference Venue

2nd q-bio Conference Satellite Workshop Participants

The following Satellite Workshop is planned for Aug 9-10:

Participants: Ueli Aebi (U. Basel), Geza Ambrus-Aikelin (Scripps Inst.), Michael Brenner (Harvard U.), Yaron Caspi (Weizmann Inst. Sci.), Michael Elbaum (Weizmann Inst. Sci.), Ramya Gamini (U. Illinois Urbana-Champaign), Dirk Gorlich (Max Planck Inst.), Loren Hough (Rockefeller U.), Tijana Jovanovic-Talisman (Rockefeller U.), Roderick Lim (U. Basel), Lingling Miao (U. Illinois Urbana-Champaign), Sigfried Musser (Texas A&M U.), Yitzhak Rabin (Bar-Ilan U.), Michael Rexach (UC Santa Cruz), Daniel Russell (UC San Francisco), Reiner Peters (U. Muenster), Jeremy Phillips (UC San Francisco), Klaus Schulten (U. Illinois Urbana-Champaign), Murray Stewart (Cambridge U.), Jaclyn Tetenbaum-Novatt (Rockefeller U.), Susan Wente (Vanderbilt U.), Paul Welch (Los Alamos Natl. Lab.), Anton Zilman (Los Alamos Natl. Lab.)

2nd q-bio Conference Poster Presenters

Poster Session 1: Thursday, August 7

(The discrepancy between the printed booklet and the list has been removed.)

  1. Rhys Adams, University of Texas M. D. Anderson Cancer Center
    Population survival, environmental fluctuations, and phenotypic switching (pdf)
  2. Eric Batchelor, Harvard Medical School
    Recurrent Initiation: A Mechanism for Triggering p53 Pulses in Response to DNA Damage (pdf)
  3. Matthew R. Bennett, University of California, San Diego - Spotlight Talk
    Modeling the genetic dual-feedback oscillator (pdf)
  4. Kevin Cahill, University of New Mexico
    Models of Cell-Penetrating Peptides (pdf)
  5. Brandon Chisham, New Mexico State University
    Analysis of the Effect of Beverage Consumption on Gene Expression in Blood (pdf)
  6. Chiraj Dalal, California Institute of Technology
    Stochastic Nuclear Localization Bursts Coordinately Regulate Target Genes (pdf)
  7. Bryan Daniels, Cornell University
    Sloppiness in Biochemical Modeling and Evolution (pdf)
  8. Mary J. Dunlop, California Institute of Technology
    Regulation Revealed by Correlations in Gene Expression Noise (pdf)
  9. James R. Faeder, University of Pittsburgh School of Medicine
    Rule-Based Modeling of Biochemical Systems with BioNetGen (pdf)
  10. Ofer Feinerman, Memorial Sloan-Kettering Cancer Center - Spotlight Talk
    IL-2 couples T lymphocytes in their activation: from single cell to population (pdf)
  11. Andrew J. Gentles, Stanford University
    Gene Module Regulatory Network Analysis of Follicular Lymphoma Transformation (pdf)
  12. Daniel Georgiev, University of Washington - Spotlight Talk
    Experimental Design of In Vitro DNA Reaction Networks (pdf)
  13. Arthur C. Goldsipe, Massachusetts Institute of Technology
    Using the DataRail toolbox to analyze inflammatory signals in U937 macrophages (pdf)
  14. Thomas G. W. Graham, University of Chicago
    Physicochemical Modeling of Antagonistic Transcriptional Regulation by Yan and Pnt (pdf)
  15. Brian Harms, Merrimack Pharmaceuticals
    Computational modeling and simulation lead to the development of MM-121, a human monoclonal antibody ErbB3 antagonist (pdf)
  16. Stephen J. Helms, University of Texas Southwestern Medical Center at Dallas -Spotlight Talk
    Implications of Dynamic Scaffolding for Signaling Efficiency in Drosophila Phototransduction (pdf)
  17. Carlos M. Herrera Jr., New Mexico State University
    Computing a Generalized Logical Network from Neural Codes (pdf)
  18. Kerwyn Casey Huang, Princeton University
    The Beginning of the Ends: Localization of Lipids to Bacterial Poles (pdf)
  19. Masayo Inoue, University of Tokyo
    Conditions for Chemotactic Behaviors both in Single Bacterium and in Interacting Aggregation (pdf)
  20. Stefan Klumpp, University of California, San Diego
    Growth-rate dependent effects on bacterial gene expression (pdf)
  21. Michal Komorowski, University of Warwick
    Reconstruction of transcriptional dynamics from gene reporter data (pdf)
  22. Fangting Li, University of California, San Francisco
    The 6-site phosphorylation of Sic1 causes a switch-like G1/S transition in budding yeast cell-cycle process (pdf)
  23. Xili Liu, University of California, San Francisco
    Construct a push-on-push-off switch in Escherichia coli (pdf)
  24. Tao Long, Princeton University -Spotlight Talk
    Single-cell Study of Bacterial Signaling in Quorum Sensing (pdf)
  25. Diane Longo, University of California, San Diego -Spotlight Talk
    Expression Variability from a Tet-inducible Positive Feedback Network in Mammalian Cells (pdf)
  26. Wenzhe Ma, University of California, San Francisco
    Design Principles of Perfect Adaptation in Biochemical networks (pdf)
  27. Luca Mariani, Humboldt University
    Chromatin dynamics in IL-4 stochastic expression (pdf)
  28. Mirjam Mayer, Max Planck Institute, Dresden
    Mechanics of Cellular Polarization in C. elegans (pdf)
  29. Pankaj Mehta, Princeton University
    Biological Constraints on Signal Integration in Bacteria (pdf)
  30. Michael Monine, Los Alamos National Laboratory
    Modeling multivalent ligand-receptor interactions with constraints on configurations of cell-surface receptor aggregates (pdf)
  31. Andrew Mugler, Columbia University
    Quantifying evolvability in small biological networks (pdf)
  32. Gregor Neuert, Massachusetts Institute of Technology
    Information processing in single yeast cells: from signal transduction to gene expression (pdf)
  33. Julien F. Ollivier, McGill University
    In silico evolution of allosteric protein modules (pdf)
  34. Gerard J. Ostheimer, Massachusetts Institute of Technology
    How Cells Decide Between Apoptosis and Permanent Arrest in Response to DNA Damage (pdf)
  35. Samuel D. Palmer, New Mexico State University
    Generalized Logical Networks of Metabolomic Interactions in Alfalfa and Medicago truncatula (pdf)
  36. Krishnan Radhakrishnan, University of New Mexico
    Decoupled Direct Method of Systematic Sensitivity Analysis: Application to Study of ERK1 Nuclear Translocation (pdf)
  37. Arjun Raj, Massachusetts Institute of Technology
    Stochastic gene expression and the partial penetrance of developmental phenotypes (pdf)
  38. Shay M. Rappaport, Bar-Ilan University
    Model of DNA Bending by Cooperative Binding of Proteins (pdf)
  39. J. Christian J. Ray, Rice University
    Design principles of bacterial chromosome organization (pdf)
  40. Bin Hu, University of New Mexico
    GetBonNie: online rule-based modeling tools (pdf)
  41. Oliver Ruebenacker, University of Conneciticut Health Center
    Towards unifying systems biology- using pathway data in BioPAX format for SBML simulators (pdf). See also [1].
  42. Carlos Salazar, German Cancer Research Center
    Multisite Protein Phosphorylation as a Molecular Timing Device (pdf)
  43. Alvaro Sanchez, Brandeis University
    Connecting mechanistic models of transcriptional regulation and single-cell gene expression data (pdf)
  44. Edda G. Schulz, Humboldt University
    Two feedback loops control Th1 differentiation (pdf)
  45. Vahid Shahrezaei, McGill University
    Colored extrinsic fluctuations and stochastic gene expression (pdf)
  46. Abhyudai Singh, University of California, Santa Barbara
    Noise suppression in auto-regulatory gene networks (pdf)
  47. Nikolai Sinitsyn, Los Alamos National Laborator
    Theoretical characterization of the efficiency of molecular motors (pdf)
  48. Michael W. Sneddon, Yale University
    NFsim: Managing Complexity in Stochastic Simulations of Reaction Networks (pdf)
  49. Soon Heng Tan, University of Toronto
    Understanding signaling network evolution: A quantitative approach (pdf)
  50. Jaclyn Tetenbaum-Novatt, Rockefeller University
    Kinetic Analysis of Nucleocytoplasmic Transport (pdf)
  51. Gandhi M. Viswanathan, University of New Mexico
    Estimation of multifractal properties of random walks observed through finite probing windows (pdf)
  52. Aleksandra M. Walczak, Princeton University - Spotlight Talk
    Gene-gene cooperativity in small networks (pdf)
  53. Yilin Wu, University of Notre Dame - Spotlight Talk
    A Computational Model for Bacterial Swarming (pdf)
  54. Yu Feng Wu, Stony Brook University
    Master equation simulation analysis of immunostained Bicoid morphogen gradient (pdf)
  55. Qiong Yang, Massachusetts Institute of Technology
    Coupled oscillators and circadian gating in the cyanobacterial circadian clock (pdf)
  56. Toru Yao, National Institute of Advanced Industrial Science and Technology
    TBA (pdf)
  57. Anton Zilman, Los Alamos National Laboratory
    Mechanisms of selective transport through nano-channels: Theory vs. experiment (pdf)
  58. Susan R. Atlas, University of New Mexico
    Systems Model for Prognostic Cancer Biology (pdf), moved from Friday.

Poster Session 2: Friday, August 8

  1. Gary C. An, Northwestern University
    TLR4 signaling and tolerance: Dynamic knowledge representation using BioNetGen (pdf)
  2. Jorge Gil C. Angeles, New Mexico State University
    Dynamic System Modeling of Gene Expression in Plant-Fungi Symbiosis (pdf)
  3. David W. Dreisigmeyer, Los Alamos National Laboratory
    Determinants of Bistability in Induction of the Escherichia coli lac Operon (pdf)
  4. Gabor Balazsi, University of Texas M. D. Anderson Cancer Center
    The causes and consequences of gene expression flexibility (pdf)
  5. Long Cai, California Institute of Technology - Spotlight Talk
    Frequency-Modulated Localization Bursts Coordinate Gene Regulation (pdf)
  6. Yaron Caspi, Weizmann Institute of Science
    A Chemical Mimic of the Nuclear Pore Complex (pdf)
  7. Hui-Chun Cheng, University of Texas Southwestern Medical Center at Dallas
    Stoichiometry Distribution of the Nephrin/Nck/WASP Signalsome (pdf)
  8. Judith Cohn, Los Alamos National Laboratory
    BIOGRAM: Identifying Similar Proteins by Functional Annotation (pdf)
  9. Cristina-Maria Dabu, Romanian Academy
    Control systems theory and neuronal modeling (pdf)
  10. Tal Danino, University of California, San Diego
    Synchronization of genetic oscillators in E. coli (pdf)
  11. Meghan Driscoll, University of Maryland
    Competing Chemical and Topographical Signals in Dictyostelium discoideum migration (pdf)
  12. Jonathan Fitzgerald, Merrimack Pharmaceuticals
    Understanding IGF signaling dynamics through computational modeling (pdf)
  13. Pak-Wing Fok, California Institute of Technology
    Guanine mediated adsorption of DNA repair enzymes (pdf)
  14. Beata Hat, Institute of Fundamental Technological Research
    Gene Copy Number in p53 Signaling Pathway (pdf)
  15. Takahiro Harada, University of Fukui
    Long-term correlation in the beat rate fluctuations of single cardiac cells (pdf)
  16. Leonard A. Harris, University of Pittsburgh School of Medicine
    Multiscale Simulation of Rule-Based Models (pdf)
  17. Sara Hooshangi, University of Maryland
    Characterization of AI-2 uptake pathway in E. coli quorum sensing circuitry (pdf)
  18. Elizabeth D. Jones, Baylor College of Medicine
    Regulation of Nuclear Receptor Mediated Transcription (pdf)
  19. Jaewook Joo, Sandia National Laboratory
    Noise-induced oscillations of NF-κB shuttling (pdf)
  20. Ziya Kalay, University of New Mexico
    An Analytic Study of Molecular Motion in Cell Membranes (pdf)
  21. Jeff Kearns, University of California, San Diego
    The Integration of Multiple Negative Feedback Regulators Directs Diverse NF-κB Signaling Dynamics (pdf)
  22. Choel Kim, University of California, San Diego - Spotlight Talk
    The First Crystal Structure of cyclic GMP-dependent protein kinase Iβ dimerization domain reveals the molecular features of an extended leucine/isoleucine zipper (pdf)
  23. Niraj Kumar, University of New Mexico
    Extinction of cellular organisms in the presence of multiple hostile and favorable environments (pdf)
  24. Sotiria Lampoudi, University of California, Santa Barbara
    Modeling raises the possibility that BvgAS phosphorelay kinase activity may be constitutive (pdf)
  25. Tomasz Lipniacki, Institute of Fundamental Technological Research
    Stochasticity and Bistability in TCR Signaling (pdf)
  26. Zhen Liu, Virginia Polytechnic Institute and State University
    A Hybrid Method Combining Improved StochSim with SSA for Solving Systems with Multistate Species (pdf)
  27. Alexander Loewer, Harvard Medical School - Spotlight Talk
    Dynamics of p53 in non-stressed conditions (pdf)
  28. Carlos Lopez, Harvard Medical School
    Understanding variability in the ErbB signaling network (pdf)
  29. Shalini T. Low-Nam, University of New Mexico
    Development of Monovalent Fluorescent Probes for Single Particle Tracking of ErbB Receptors (pdf)
  30. Oded Maler, CNRS-Verimag
    TBA (pdf)
  31. Carlos Martinez, Stony Brook University
    In Silico Evolution of Even-skipped Stripe 2 (pdf)
  32. Osorio Meirelles, University of New Mexico
    Robust Estimation of Microarrays (pdf)
  33. Alexander Y. Mitrophanov, Washington University School of Medicine
    Regulatory architectures and dynamics of bacterial gene expression (pdf)
  34. Fangping Mu, Los Alamos National Laboratory
    Prediction of enzyme-catalyzed reactions based on atomic and molecular properties of metabolites (pdf)
  35. Ambarish Nag, Los Alamos National Laboratory - Spotlight Talk
    How does a mast cell distinguish between two different extracellular stimuli that cause the same extent of receptor cross-linking? (pdf)
  36. Dmitry Nevozhay, University of Texas M. D. Anderson Cancer Center
    The effect of negative feedback strength on gene expression noise (pdf)
  37. Torbjoern E. M. Nordling, Royal Institute of Technology
    Ill-conditioning – a property of bio-networks (pdf)
  38. Zhengyu Ouyang, New Mexico State University
    Evaluation in Dynamic System Modeling of Gene Networks (pdf)
  39. Bernardo Pando, Massachusetts Institute of Technology
    Predicting bistable gene expression through input-output transfer functions (pdf)
  40. William Pontius, Yale University - Spotlight Talk
    An integrated analytic model of bacterial chemotaxis (pdf)
  41. Krzysztof Puszynski, Silesian University of Technology
    Stochastic Robustness of NF-κB signaling (pdf)
  42. Indika Rajapakse, Fred Hutchinson Cancer Research Center
    Dynamics of genetic organization: Hematopoietic system (pdf)
  43. Daniel Reeves, Brandeis University
    Physics of Formin Regulated Actin Growth (pdf)
  44. Sushmita Roy, University of New Mexico - Spotlight Talk
    Scalable learning of large networks (pdf)
  45. Karen Sachs, Stanford University
    Learning drug targets in the signaling network context (pdf)
  46. Julio Saez-Rodriguez, Harvard Medical School
    Interrogating topology of signaling networks with large-scale data within a Boolean framework (pdf)
  47. Jakob Schluttig, University of Heidelberg
    Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches (pdf)
  48. Richard P. Sear, University of Surrey
    Cell signaling and virus restriction via phase separation in the cytoplasm (pdf)
  49. Elba E. Serrano, New Mexico State University
    Construction of Integrative Cross-Platform Databases for Organ Systems and Development (pdf)
  50. Charlie E. M. Strauss, Los Alamos National Laboratory
    On the origin of symmetry in biological macromolecules (pdf)
  51. Yuichi Taniguchi, Harvard University
    Single-cell Analysis of the Escherichia coli Proteome with Single-Molecule Sensitivity (pdf)
  52. Jose Teles, Lund University
    Inference and dynamical modeling of regulatory networks controlling hematopoiesis (pdf)
  53. Erik S. Welf, University of Delaware - Spotlight Talk
    Regulation of Integrin Clustering: Models and Experiments (pdf)
  54. David Wu, California Institute of Technology
    An information-theoretic approach to distributions of trajectories (pdf)
  55. Tianyi Yang, University of Texas
    Cell adhesion to motile nano ligands: Effects of ligand size and concentration in solution (pdf)
  56. Xiaojing Yang, University of California, San Francisco - Spotlight Talk
    Quantitatively monitoring the G1stability in single cell (pdf)
  57. Lech Znamirowski, Silesian University of Technology
    Replication and Self-assembly Concatenation Control in the Nanoprocesses (pdf)
  58. Andrea Asztalos, University of Notre Dame
    Protein folding topology from conformation networks (pdf)

Information for Presenters

  • If your accepted poster is missing from this page, or if there is a problem with its listing, please notify the organizers by email.
  • Your poster number, which you will need to locate the poster board assigned to you, is the number listed above next to your poster title. This number may change before August 1, 2008 but it will be fixed after the 1st.
  • Set up your poster during the lunch break on the day of your presentation. Please use the recommended method to hang your poster (more later). Poster boards will be located in the Junior and Senior Rooms, which are adjacent to the Great Hall.
  • Poster boards have a portrait orientation: 4 feet (120 cm) wide by 6 feet (180 cm) tall.
  • Poster presenters are expected to be at their posters from 20:30 to 22:00 on the day of their presentation. Please be available to present your work during this time. Beverage and food service ends at 23:00; the poster session ends at midnight.
  • Remove your poster before the end of the first coffee break on the day following your presentation and no earlier than midnight on the day of your presentation.

2nd q-bio Conference Other Participants

  1. Roger Alexander, Yale University
  2. Roee Amit, California Institute of Technology
  3. Andrea Asztalos, University of Notre Dame
  4. Pradeep Bandaru, Columbia University
  5. Golan Bel, Los Alamos National Laboratory
  6. Josh Bishop, University of Washington
  7. Naama Brenner, Technion
  8. Martha Bulyk, Harvard Medical School
  9. Yang Cao, Virginia Polytechnic Institute and State University
  10. Seth Difley, Massachusetts Institute of Technology
  11. Robert Ecke, Los Alamos National Laboratory
  12. Thierry Emonet, Yale University
  13. Richard Fagerstrom, National Cancer Institute
  14. Byron Goldstein, Los Alamos National Laboratory
  15. Loren Hough, Rockefeller University
  16. Oleg Igoshin, Rice University
  17. Yi Jiang, Los Alamos National Laboratory
  18. Nitant Kenkre, University of New Mexico
  19. Eric Klavins, University of Washington
  20. Andre Levchenko, Johns Hopkins University
  21. Bryan Linggi, Merrimack Pharmaceuticals
  22. Ilya Nemenman, Los Alamos National Laboratory
  23. Alan Perelson, Los Alamos National Laboratory
  24. Maria Pospieszalska, La Jolla Institute for Allergy & Immunology
  25. Orna Resnekov, Molecular Sciences Institute
  26. Hanna Salman, University of Pittsburgh
  27. Chris Wiggins, Columbia University
  28. Yang Zhang, New Mexico State University
  29. Artur Znamirowski, Warsaw University of Technology

2nd q-bio Conference Speakers Presenting Spotlight Talks

  1. Matthew R. Bennett, University of California, San Diego
    Modeling the genetic dual-feedback oscillator (pdf)
  2. Long Cai, California Institute of Technology
    Frequency-Modulated Localization Bursts Coordinate Gene Regulation (pdf)
  3. Ofer Feinerman, Memorial Sloan-Kettering Cancer Center
    IL-2 couples T lymphocytes in their activation: from single cell to population (pdf)
  4. Daniel Georgiev, University of Washington
    Experimental Design of In Vitro DNA Reaction Networks (pdf)
  5. Stephen J. Helms, University of Texas Southwestern Medical Center at Dallas
    Implications of Dynamic Scaffolding for Signaling Efficiency in Drosophila Phototransduction (pdf)
  6. Choel Kim, University of California, San Diego
    The First Crystal Structure of cyclic GMP-dependent protein kinase Iβ dimerization domain reveals the molecular features of an extended leucine/isoleucine zipper (pdf)
  7. Alexander Loewer, Harvard Medical School
    Dynamics of p53 in non-stressed conditions (pdf)
  8. Tao Long, Princeton University
    Single-cell Study of Bacterial Signaling in Quorum Sensing (pdf)
  9. Diane M. Longo, University of California, San Diego
    Expression Variability from a Tet-inducible Positive Feedback Network in Mammalian Cells (pdf)
  10. Ambarish Nag, Los Alamos National Laboratory
    How does a mast cell distinguish between two different extracellular stimuli that cause the same extent of receptor cross-linking? (pdf)
  11. William Pontius, Yale University
    An integrated analytic model of bacterial chemotaxis (pdf)
  12. Sushmita Roy, University of New Mexico
    Scalable learning of large networks (pdf)
  13. Charlie E.M. Strauss, Los Alamos National Laboratory
    On the origin of symmetry in biological macromolecules (pdf)
  14. Aleksandra M. Walczak, Princeton University
    Gene-gene cooperativity in small networks (pdf)
  15. Erik S. Welf, University of Delaware
    Regulation of Integrin Clustering: Models and Experiments (pdf)
  16. Yilin Wu, University of Notre Dame
    A Computational Model for Bacterial Swarming (pdf)
  17. Xiaojing Yang, University of California, San Francisco
    Quantitatively monitoring the G1stability in single cell (pdf)

© 2017 New Mexico Consortium