Welcome to the q-bio Summer School and Conference!

The Eighth q-bio Conference: Program Overview

From Q-bio
Thanks for attending The Eighth q-bio Conference
the annual conference dedicated to
advancing quantitative understanding of cellular regulation

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?