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The Eighth q-bio Conference: Program Overview
From Q-bio
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Contents
Venue information
This map of the Peterson Student Center building may be helpful.
Wednesday, August 13
Session 1: Tutorial Session (in Great Hall, SCR, and JCR), 12:00 - 18:00
- 12:00-14:00 James Faeder, University of Pittsburgh, Modeling Complex Biochemical Systems in Time and Space Using BioNetGen and MCell (Great Hall) (slides & materials)
- 14:00-16:00 Steve Andrews, Fred Hutchinson Cancer Center, Smoldyn: Spatial Cell Biology Simulation (Great Hall) (slides)
- 16:00-18:00 Carlos Lopez, Vanderbilt University, PySB, a programming environment to generate algorithmic representations of biological systems (Great Hall) (slides)
- 12:00-14:00 Gerard Ostheimer, UN Sustainable Energy For All, Partial Least Squares Regression (PLSR) for the Discovery of New Biology (SCR)
- 14:00-16:00 Ilya Nemenman, Emory University, Noise and Information Transmission (SCR)
- 14:00-16:00 Eric Mjolsness, UC Irvine, Biosystem modeling methods at multiple scales (JCR)
- 16:00-18:00 Martin Meier-Schellersheim, NIH/NIAID, Designing and simulating cellular signaling networks with Simmune (JCR) (software link)
Session 2: Opening Banquet (19:00 - 21:00, Dining Hall)
- 19:00-19:10 Introduction and Welcome, Jim Faeder, University of Pittsburgh
- 19:10-19:15 New Mexico and q-bio, Bridget Wilson, University of New Mexico
- 19:15-19:20 q-bio Summer School Recap, Brian Munsky, Colorado State University
- 19:20-19:25 q-bio Special Issue, Ilya Nemenman, Emory University
- 19:20-20:00 Dinner
- 20:00-20:05 Banquet Speaker Introduction, William S. Hlavacek, Leor Weinberger
- 20:05-21:00 Banquet Talk, Alan S. Perelson, Los Alamos National Laboratory, How Modeling Viral Infections Can Save Lives
Thursday, August 14
7:30-9:00 Breakfast (Dining Hall)
Session 3 (9:00-12:20, Great Hall)
- Chair: James Faeder, University of Pittsburgh Medical School
- 9:00-9:30 Invited talk 1, Naama Barkai, Weizmann Institute of Science, Robust periodic patterning in the Drosophila eye
- 9:30-9:50 Contributed talk 1, Jian Liu, NIH, Traction peak oscillation optimizes focal adhesion mechanosensing
- 9:50-10:20 Invited talk 2, Nathalie Dostani, Institut Curie, Transcriptional dynamics in the early Drosophila embryo
10:20-10:50 Coffee Break
- 10:50-11:10 Poster Spotlights I
- Poster Spotlight 1, Kevin Brown, University of Connecticut, Mean-Field Approaches to Protein Evolution
- Poster Spotlight 2, Jonathan Desponds, ENS, Paris, France, Effect of random environments on clone size distributions of the immune repertoire
- Poster Spotlight 3, M. Frank Erasmus, University of New Mexico, Role for the pre-BCR Signaling Complex in BCP-ALL Blast Cell Survival
- Poster Spotlight 4, Sidney Kuo, UCSD, Variability of hyperosmotic stress response via the HOG pathway in wild yeast strains
- 11:10-11:40 Invited talk 3, Diane Lidke, University of New Mexico, Measuring EGFR dynamics, dimerization and conformation on live cells
- 11:40-12:00 Contributed talk 2, John Albeck, UC Davis, Linking localized ERK/MAPK dynamics to transcriptional network states
- 12:00-12:20 Contributed talk 3, Will Mather, Virginia Tech, A queueing approach to multisite enzyme kinetics
12:20-14:30 Lunch (Dining Hall)
Session 4 (14:30-18:10, Great Hall)
- Chair: Michael Wall, Los Alamos National Laboratory
- 14:30-14:35 Introduction of Pioneer Speaker, S. Gnanakaran, Los Alamos National Laboratory
- 14:35-15:20 Pioneer Talk, Greg Voth, University of Chicago, Theory and Simulation of Biomolecular Systems: The Multiscale Challenge
- 15:20-15:40 Contributed talk 4, Christopher Cotter, University of Georgia, Quantification and Modeling of the self-organization of Myxococcus xanthus
- 15:40-16:10 Invited talk 4, Markus W. Covert, Stanford University, High-sensitivity measurements of multiple kinase activities in live single cells
16:10-16:40 Coffee Break
- 16:40-17:00 Poster Spotlights II
- Poster Spotlight 5, Yuval Elhanati, CNRS and ENS, Paris, France, Identifying selection pressures in somatic immune receptor evolution
- Poster Spotlight 6, Nicola Gritti, AMOLF, Rolling dice during development: Timelapse microscopy of stochastic cell fate decisions in C. elegans
- Poster Spotlight 7, Xiuxiu He, Georgia State, Modeling 3D Cell Migration
- Poster Spotlight 8, Mohit Kumar Jolly, Rice University, Modeling the Association between Epithelial-Mesenchymal Transition (EMT) and Stemness
- 17:00-17:30 Invited talk 5, Shayne Peirce-Cottler, University of Virginia, Multiscale Models of Tissue Growth and Remodeling
- 17:30-17:50 Contributed talk 5, Jianhua Xing, Virginia Tech, A cascade of bistable switches controls TGF-beta induced epithelial-to-mesenchymal transition
- 17:50-18:10 Contributed talk 6, Andrew Paek, Harvard Medical School, Single cell analysis reveals a time-dependent threshold for p53 mediated apoptosis
18:10-20:00 Dinner in town (no meal service at St. John's)
Session 5 (20:00-23:00, Poster Session I, JCR and Fireside Lounge)
- 20:00-23:00 Poster Session I (snacks and drinks served)
Friday, August 15
7:30-9:00 Breakfast (Dining Hall)
Session 6 (9:00-12:20, Great Hall)
- Chair: Yi Jiang, Georgia State
- 9:00-9:30 Invited talk 6, Peter Sorger, Harvard Medical School, Measuring and Modeling Cell Death Pathways in Single Cells
- 9:30-9:50 Contributed talk 7, Tomasz Lipniacki, IFTR- Poland, NF-κB and IRF3 crosstalk signaling in MEFs
- 9:50-10:20 Invited talk 7, Kwang-Hyun Cho, Korea Advanced Institute of Science & Technology, The regulation of uncontrolled cell proliferation by hidden switches mediated by RORα
10:20-10:50 Coffee Break
- 10:50-11:10 Poster Spotlights III
- Poster Spotlight 9, Gabriele Micali, Imperial College, Predicting chemical environments from receptor signaling
- Poster Spotlight 10, Andreas Mayer, LPT ENS, Design Principles of an Optimal Adaptive Immune System
- Poster Spotlight 11, Shlomi Reuveni, Harvard University, The role of substrate unbinding in Michaelis-Menten enzymatic reactions
- Poster Spotlight 12, Leili Shahriyari, UC Irvine, Symmetric vs. Asymmetric Stem Cell Divisions
- 11:10-11:40 Invited talk 8, Alex Mogilner, UC Davis, Modules of Cell Polarization/Motility Initiation
- 11:40-12:00 Contributed talk 8, Andrew Mugler, Emory, Fundamental limits to the precision of multicellular sensing
- 12:00-12:20 Contributed talk 9, Mikhail Tikhonov, Princeton University, Cascading Non-Local Noisy Readouts Improves Precision of Gradient Response
12:20-14:30 Lunch (Dining Hall)
Session 7 (14:30-17:40, Great Hall)
- Chair: Orna Resnekov, Molecular Sciences Institute
- 14:30-15:00 Invited talk 9, Paulien Hogeweg, Utrecht University, Modeling Multilevel Evolution: qualitative modeling for quantitative insights
- 15:00-15:20 Contributed talk 10, Nicole Vega, MIT, Population dynamics of cooperative antibiotic resistance in a C. elegans model
- 15:20-15:40 Contributed talk 11, John Pearson, LANL, Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient
15:40-16:10 Coffee Break
- 16:10-16:30 Poster Spotlights IV
- Poster Spotlight 13, Vijay Singh, Emory University, Information transmission by receptors correlated through ligand diffusion
- Poster Spotlight 14, Noreen Walker, AMOLF, Gene expression noise: How much is explained by growth fluctuations?
- Poster Spotlight 15, Roy Wollman, UCSD, Accurate information transduction in dynamic biochemical signaling networks
- Poster Spotlight 16, Alon Yaniv, Ben-Gurion University, Spatial Effects in Cytokine Signaling Between T Cells
- 16:30-17:00 Invited talk 10, Nicolas Desprat, École Normale Superieure, Spatial interactions in bacterial colonies
- 17:00-17:20 Contributed talk 12, Savas Tay, ETH, Molecular noise facilitates NF-κB entrainment under dynamic inputs
- 17:20-17:40 Contributed talk 13, Ivan Surovtsev, Yale University, Physical Nature of the Bacterial Cytoplasm
Session 8 (18:00-20:00, Koi Pond)
- 18:00-19:00 Dinner (service at Koi Pond)
- 19:00-20:00 Special session, Paul Cohen, DARPA, Overview of the Big Mechanism Program (Great Hall)
Session 9 (20:00-23:00, Poster Session II, JCR and Fireside Lounge)
- 20:00-23:00 Poster Session II (snacks and drinks served)
Saturday, August 16
7:30-9:00 Breakfast (Dining Hall)
Session 10 (9:00-12:10, Great Hall)
- Chair: Anton Zilman, University of Toronto
- 9:00-9:30 Invited talk 11, Arthur D. Lander, University of California, Irvine, The Engineering of Growth Control
- 9:30-9:50 Contributed talk 14, Jennifer Oyler, Cornell University, mRNA as a molecular clock: how mRNA longevity controls the persistence of cellular information
- 9:50-10:10 Contributed talk 15, Judy Cannon, University of New Mexico, T cell motility within lymph nodes are more consistent with a correlated random walk than a Levy walk
- 10:10-10:30 Contributed talk 16, Shao Qiuyan, Texas A&M, Phage DNA dynamics and the Correlation with Cell Fate
10:30-11:00 Coffee Break
- 11:00-11:30 Invited talk 12, Linda Petzold, UC Santa Barbara, Stochastic Simulation at Your Service
- 11:30-11:50 Contributed talk 17, Carlos Lopez, Vanderbilt, Model-driven exploration of apoptosis or necroptosis cell-death decisions
- 11:50-12:10 Contributed talk 18, Jason Lomnitz, UC Davis, Phenotypic Differences Among Seven Synthetic Oscillator Designs
- 12:10-12:30 Contributed talk 19, Hanna Salman, University of Pittsburgh, Protein Fluctuations in Single Cells and Population Variability
12:30-14:30 Lunch
Session 11 (14:30-17:50, Great Hall)
- Chair: S. Gnanakaran, Los Alamos National Laboratory
- 14:30-15:00 Invited talk 13, Bridget S. Wilson, University of New Mexico School of Medicine, Orchestration of erbB3 signaling through homo-dimerization and hetero-dimerization with erbB2.
- 15:00-15:20 Contributed talk 20, Daniel DeWoskin, University of Michigan, Fast and Slow Coupling in the Circadian Clock
- 15:20-15:40 Contributed talk 21, Jenny Lin, University of Chicago, Mixtures of opposing phosphorylations within hexamers precisely time feedback in the cyanobacterial circadian clock
- 15:40-16:00 Contributed talk 22, Oleg Igoshin, Rice University, Slowdown of cell growth acts as the signal triggering cellular differentiation
16:00-16:30 Coffee Break
- 16:30-17:00 Invited talk 14, Thierry Emonet, Yale University, Diversified population strategies for chemotaxis trade-off problems
- 17:00-17:20 Contributed talk 23, David Fange, Uppsala University, In vivo repressor kinetics exclude simple operator occupancy model for gene regulation
- 17:20-17:40 Contributed talk 24, Arvind Subramaniam, Harvard University, Amino Acid Starvation Reveals Constraints for Modeling Translation
- 17:40-18:00 Contributed talk 25, Brian Munsky, Colorado State, Transcription factors modulate c-Fos transcriptional bursts
Session 12: Closing Banquet (18:30-20:45, Dining Hall)
- 18:30-18:35 Acknowledgments, Bill Hlavacek, Los Alamos National Lab
- 18:35-18:40 Closing remarks, Bob Ecke, Director of the Center for Nonlinear Studies, Los Alamos National Laboratory
- 18:40-18:45 Long live q-bio!, Jim Faeder, University of Pittsburgh
- 18:45-18:50 Introduction of q-bio 2015, Will Mather, Virginia Tech
- 18:30-19:45 Dinner
- 19:45-19:50 Banquet Speaker Introduction, Ilya Nemenman, Emory University
- 19:50-20:45 Banquet Talk, William Bialek, Princeton University, Are we asking the right questions?
