The Third q-bio Conference: Poster Presenters

Back to The Third q-bio Conference.

Note to organizers: do not make any changes that would alter the poster numbers.

Poster Session 1: Thursday, August 6

1. Rhys M. Adams, University of Texas M.D. Andersen Cancer Center
   Design principles of synthetic gene circuits based on the TetR family of regulators (pdf) - Spotlight Talk
2. Justin S. Hogg, University of Pittsburgh School of Medicine
   Rule-based modeling of sepsis (pdf)
3. Gerard J. Ostheimer, Massachusetts Institute of Technology
   To sleep or die: cell fate after chemotherapy (pdf)
4. Stanly Steinberg, University of New Mexico
   Time series analysis of particle tracking data for molecular motion on the cell membrane (pdf)
5. Bryan C. Daniels, Cornell University
   Discontinuities at the DNA supercoiling transition (pdf)
6. Volkan Sevim, Duke University
   Stabilizing motifs in autonomous Boolean networks and the yeast cell-cycle oscillator (pdf)
7. Richard I. Joh, Georgia Institute of Technology
   Nonlinear dependence in gene expression on gene copy number in regulatory network motifs (pdf)
8. Andrew Mugler, Columbia University
   Mesoscopic statistical properties of multistep enzyme-mediated reactions (pdf) - Spotlight Talk
9. Srabanti Chaudhury, Rice University
   Dynamic disorder driven substrate inhibition and bistability in simple enzymatic reaction (pdf)
10. Gabriel J. Mitchell, Georgia Institute of Technology
    Characterizing bacterial lysis by phage lytic enzymes using non-parametric data collapse (pdf)
11. Elena E. Giorgi, University of Massachussetts
    Age-structured stochastic model of intrapatient HIV evolution (pdf)
12. Lanying Zeng, University of Illinois, Urbana-Champaign
    Decision-making in bacteriophage lambda: a view from the single phage (pdf)
13. Nikolai A. Sinitsyn, Los Alamos National Laboratory
    The theory of non-autonomous molecular motor motion (pdf)
14. T. Lance Min, University of Illinois, Urbana-Champaign
    Optical-trap based analysis of bacterial motility (pdf)
15. Verena Wolf, EPFL, Switzerland
    Solving the chemical master equation using creeping windows (pdf) - Special Session Talk
16. Moshe Naoz, Weizmann Institute of Science
    A physical minimalistic model for podosomes (pdf)
17. Ryan N. Gutenkunst, Los Alamos National Laboratory
    Proteins that have a large influence on network dynamics evolve slowly (pdf)
18. Bin Hu, University of New Mexico
    GetBonNie for building, analyzing and sharing rule-based models (pdf)
19. James H. Werner, Los Alamos National Laboratory
    Confocal, 3D tracking of individual quantum dot labeled signaling molecules on live cells (pdf) - Special Session Talk
20. Pau Formosa-Jordan, Universitat de Barcelona
    Diffusible ligand and lateral inhibition dynamics for pattern formation (pdf)
21. Jatin Narula, Rice University
    Design principles of the regulatory module in hematopoietic differentiation network (pdf)
22. Michael T. Beste, University of Pennsylvania
    Inside-out signal integration and integrin activation during T lymphocyte recruitment (pdf)
23. Daniel Andor-Ardó, Rockefeller University
    Biological oscillators with autocatalytic steps: resonant release of synaptic transmitter (pdf) - Spotlight Talk
24. Gabriele Lillacci, University of California, Santa Barbara
    Parameter estimation and model selection in computational biology (pdf) - Spotlight Talk, Satellite Workshop Talk
25. Amy L. Bauer, Los Alamos National Laboratory
    Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites (pdf)
26. Brian Drawert, University of California, Santa Barbara
    Stochastic modeling and simulation of cell polarization during mating in budding yeast (pdf)
27. André Leier, Swiss Federal Institute of Technology (ETH) Zürich
    Probability distributed time delays: integrating spatial effects into temporal models (pdf)
28. Golan Bel, Los Alamos National Laboratory
    Specificity and first passage times of common biochemical processes (pdf) - Spotlight Talk
29. Chien-Chi Lo, Los Alamos National Laboratory
    A software tool to process HIV ultra-deep sequencing nucleotide data (pdf)
30. Alan Waggoner, Carnegie Mellon University
    Fluorescent biosensors for cell regulation pathways (pdf) - Special Session Talk
31. Mingjun Zhang, University of Tennessee
    Bio-inspired event-based game theoretical control for complex systems (pdf)
32. Srividya Iyer-Biswas, Ohio State University
    The role of time scales in extrinsic noise propagation (pdf)
33. Timothy Saunders, John Innes Center, Norwich
    Morphogen profiles can be optimized to buffer against noise (pdf)
34. Pablo Meyer, Columbia University Medical School
    Cellular organization of a metabolic pathway (pdf) - Spotlight Talk
35. Richard G. Posner, Translational Genomics Research Institute
    DYNSTOC for simulating large-scale rule-based models (pdf)
36. Marcelo Behar, University of California, San Diego
    Transfer of dynamically encoded information in the NF-κB signaling network (pdf) - Spotlight Talk
37. Alissa M. Weaver, Vanderbilt School of Medicine
    Tumor Progression associated with microenvironmental independence: results from a joint experimental-mathematical study (pdf)
38. Ty M. Thomson, Plectix BioSystems
    Scalable methods for modeling complex cell signaling systems (pdf)
39. Boian Alexandrov, Los Alamos National Laboratory
    Breathing signature of the core promoter (pdf)
40. Thomas Sokolowski, AMOLF
    Using GFRD to study pattern formation due to the interplay of active and passive transporrt (pdf)
41. Michelle Costa, University of New Mexico
    Understanding the impact of IFNγR clustering on immune response pathways (pdf)
42. Elizabeth D. Jones, Rice University
    Cell cycle effects on androgen receptor functions (pdf)
43. Irakli Loladze, University of Nebraska
    Molecular origins of Redfield ratio and convergence of N:P to approximately 16 through evolution and upwelling (pdf)
44. David Basanta, H. Lee Moffitt Cancer Center
    The role of tumour heterogeneity and TGF-β mediated stromal interactions in prostate cancer (pdf)
45. Bernie J. Daigle, Jr., Stanford University School of Medicine
    Using pre-existing microarray datasets to increase experimental power: application to insulin resistance (pdf)
46. Yuki Kimura, University of Illinois, Urbana-Champaign
    The role of directional persistence in neutrophil chemotaxis: navigation in multiple gradients (pdf)
47. Aviv Madar, New York University
    Inferring topology and dynamical properties of genome-wide regulatory networks (pdf)
48. Joshua Socolar, Duke University
    Modeling cell fate specification in the sea urchin embryo (pdf) - Spotlight Talk
49. Fiona A. Chandra, California Institute of Technology
    Theoretical performance limit of the autocatalytic glycolysis system (pdf) -Satellite Workshop Talk
50. Pedro M. B. M. Coelho, University of Coimbra
    Global tolerance of biochemical systems and the design of moiety-transfer cycles (pdf)
51. C. M. Dabu, Romanian Committee of the History and Philosophy of Science and Technology, Bucharest
    Simulink model for the Ca²⁺ as second messenger in the neuronal cell (pdf)
52. Lili Jiang, Peking University
    A mechanism for precision-sensing via a gradient-sensing pathway: a model of E. coli thermotaxis (pdf)
53. Andrew H. A. Clayton, Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch
    Predominance of activated EGFR higher-order oligomers on the cell surface (pdf)
54. Anton Zilman, Los Alamos National Laboratory
    Selective transport through nano-channels: from nucleo-cytoplasmic exchange to bio-sensors (pdf)
55. Ayeeshik Kole, Vanderbilt University
    Monitoring of real-time protein concentrations in cellular yeast secretomes (pdf)

Poster Session 2: Saturday, August 8

56. Howard Salis, University of California, San Francisco
    Predicting and controlling translation rate in bacteria (pdf) - Spotlight Talk, Satellite Workshop Talk
57. Tamar Friedlander, Technion - Israel Institute of Technology
    Adaptation by state-dependent inactivation (pdf)
58. Cheemeng Tan, Duke University
    Emergent bistability by a growth-modulating positive feedback circuit (pdf)
59. Roberto L. Bertolusso, Rice University
    bioPN: an R library of C functions for simulation of stochastic biochemical reactions using Petri nets (pdf)
60. Sushmita Roy, University of New Mexico
    Learning condition-specific networks (pdf)
61. David W. Dreisigmeyer, University of Pittsburgh
    A mult-reservoir model of influenza evolution (pdf)
62. Kana Ishimatsu, University of Tokyo
    Emergence of traveling waves in the segmentation clock (pdf)
63. Hyun Youk, Massachusetts Institute of Technology
    Balancing sensing and uptake of glucose in yeast (pdf) - Spotlight Talk
64. Brian Munsky, Los Alamos National Laboratory
    Listening to the noise: random fluctuations reveal gene network parameters (pdf) - Satellite Workshop Talk
65. Lon Chubiz, University of Illinois, Urbana-Champaign
    Coordinated regulation of multiple-antibiotic resistance in Escherichia coli (pdf) - Contributed talk
66. Dmitry Nevozhay, University of Texas M. D. Anderson Cancer Center
    Precise regulation of gene expression by negative feedback (pdf) - Spotlight Talk
67. Dragos Amarie, Indiana University
    Microfluidics devices integrating microcavity surface plasmon resonance biosensors: glucose oxidase enzymatic activity (pdf) - Special Session Talk
68. Yang Zhang, New Mexico State University
    Detecting differential interactions during cell cycle exit in Drosophila wing development using comparative generalized logical modeling (pdf)
69. Tae J. Lee, Duke University
    Temporal dynamics in cell cycle entry (pdf)
70. Ganhui Lan, IBM T.J. Watson Research Center
    Distinguish, remember and adapt to environments: a strategy to survive (pdf)
71. Hao Chang, Johns Hopkins University
    Beta-arrestin assisted signal amplification during cell chemotaxis (pdf)
72. S.M.A. Tabei, University of Chicago
    Numerical study of the immune response to viral infections with self-similar epitopes (pdf)
73. Bogdan Kazmierczak, Institute of Fundamental Technological Research
    Spatial gradients in kinase activity regulation (pdf)
74. Aleksandra M. Walczak, Princeton University
    Information processing in gene regulatory cascades (pdf) - Spotlight Talk
75. Tin Y. Pang, Stony Brook University
    Toolbox model of evolution of prokaryotic metabolic networks and their regulation (pdf)
76. Stephen J. Helms, University of Texas Southwestern Medical Center
    Regulatory mechanisms of dynamic scaffolding in Drosophila phototransduction (pdf) - Contributed Talk
77. Chenghang Zong, University of Illinois, Urbana-Champaign
    Predicting the stability of an epigenetic state (pdf) - Spotlight Talk
78. Giovanni Meacci, IBM T.J. Watson Research Center
    Dynamics of the bacterial flagellar motor with multiple stators (pdf)
79. David Thorsley, University of Washington
    Observers for stochastic chemical kinetics (pdf) - Satellite Workshop Talk
80. Christian L. Barrett, University of California, San Diego
    An integration framework for multiple high-throughput measurement types (pdf)
81. Rick A. Fasani, University of California, Davis
    Finding the steady states of nonlinear systems using the canonical S-system form (pdf)
82. Dean A. Tolla, University of California, Davis
    Growth rate effects on global regulation of E. coli oxygen sensing (pdf) - Spotlight Talk
83. Oliver Ruebenacker, University of Connecticut Health Center
    Latest from the data integration frontier: using pathway data to build and annotate systems biology models (pdf) - Tutorial Talk
84. Fangping Mu, Los Alamos National Laboratory
    In silico prediction of xenobiotic metabolism in humans (pdf)
85. Michael D. Malik, University of New Mexico
    Hyperspectral line scanning microscopy for high-speed multicolor quantum dot tracking (pdf)
86. Adel Dayarian, Rutgers - The State University of New Jersey
    Epigenetic chromatin silencing (pdf)
87. David Noren, Johns Hopkins University
    Single cell analysis and mathematical description of intracellular calcium regulation through VEGF signaling (pdf)
88. Philippos Tsourkas, University of California, Davis
    Affinity discrimination in B cells requires kinetic proofreading (pdf) - Spotlight Talk
89. Jintao Liu, University of Pittsburgh School of Medicine
    Intrinsic protein disorder and protein function (pdf)
90. François St-Pierre, Stanford University
    Determination of cell fate during phage lambda infection (pdf)
91. Guang Yao, Duke University
    The Rb-E2F pathway serves as a digital counter to enable precise response to transient growth signals (pdf)
92. Ben Machta, Cornell University
    Critical points in biological membranes (pdf)
93. David Ellison, Johns Hopkins University
    Computational model and microfluidic platform for the investigation of paracrine and autocrine signaling in mouse embryonic stem cells (pdf) - Satellite Workshop Talk
94. Patrick W. Sheppard, University of California, Santa Barbara
    Low variability estimators for sensitivity analysis of stochastic biochemical reaction systems (pdf)
95. Gašper Tkačik, University of Pennsylvania
    Optimizing information flow in small genetic networks (pdf) - Spotlight Talk
96. Alex Groisman, University of California, San Diego
    Quantitative studies of bacteria in microfluidic devices (pdf) - Satellite Workshop Talk
97. A. J. Rhee, Johns Hopkins University
    Information processing in the TNF-stimulated NF-κB and JNK signaling in fibroblasts: what can thousands of little cells tell you? (pdf)
98. Octavio Mondragón-Palomino, University of California, San Diego
    Entrainment of synthetic genetic oscillators in E. coli to an external periodic signal (pdf)
99. Joseph X. Zhou, Max Planck Institute for the Physics of Complex Systems, Desden
    Gene regulatory network model of pancreatic cell differentiation and reprogramming (pdf)
100. Allan Lazarovici, Columbia University
     Statistical mechanical modeling of protein-DNA interactions (pdf)
101. Kevin Cahill, University of New Mexico
     Do phosphatidylserines transduce cell-penetrating peptides by electroporation? (pdf)
102. Pablo Sartori, IBM T.J. Watson Research Center
     Noise in bacterial chemotaxis (pdf)
103. Todd R. Riley, Columbia University
     Binding-site affinity modeling of positional dependencies and context-sensitive nucleotide insertions and deletions (pdf)
104. Ying-Ja Chen, University of California, San Diego
     Simulations and Experiments for DNA Sequencing by Denaturation (pdf) - Special Session Talk
105. Paul Loriaux, University of California, San Diego
     Static versus dynamic control of TNF-induced apoptosis by NF-κB and JNK (pdf)
106. Maria K. Pospieszalska, La Jolla Institute for Allergy and Immunology
     Dynamics of microvillus deformation in rolling leukocytes (pdf)
107. Gordon Webster, Plectix BioSystems
     Modeling dysregulation of complex systems implicated in cancer and diabetes (pdf)
108. Alex Greenfield, New York University
     Comparative genomics with cMonkey: integrative biclustering of multiple species (pdf)
109. Anton Zilman, Los Alamos National Laboratory
     Combining quantitative experiments and modeling to understand kinetics of T cell response (pdf)
110. Michael I. Monine, Los Alamos National Laboratory
     Modeling the FcεRI signaling cascade: from receptor aggregation to the oligomerization of the scaffolding protein LAT (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 name. This number may change before July 27, 2009 but it will be fixed after July 27.

• Set up your poster during the lunch break on the day of your presentation (Thursday, August 6 for Poster Session 1 or Saturday, August 8 for Poster Session 2). Please use the recommended method to attach your poster to the cloth poster boards - velcro stickers will be available. 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 23:30 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.