The Ninth q-bio Conference: Program Overview

Welcome to The Ninth q-bio Conference the annual conference dedicated to advancing quantitative understanding of cellular regulation

Dates: August 5-8, 2015 Place: Virginia Tech, Blacksburg, Virginia, USA Abstract Submission: closed.

Venue information

Please refer to the main Venue Information page, which provides general information but also information on wifi access, parking, and shuttle service. Also refer to that page if you are arriving to campus on Tuesday. A local map of the Virginia Tech campus indicating key locations is available.

If you want to know what the main entrance of Squires Student Center looks like, see https://www.vt.edu/about/buildings/squires-student-center.html.

PDF Version of the Program

A PDF version of the program is available here.

Wednesday, August 5

Registration (12:00 - 13:30, Squires Student Center and 18:00 - 19:00, The Inn at Virginia Tech)

In the morning, please register at the primary conference location, the Squires Student Center. In the evening, please register at the banquet location, The Inn at Virginia Tech.

Session 1: Tutorial Session (13:00 - 18:00, Squires Student Center, check at registration for rooms)

Session 1A - 13:00-14:30 (2 parallel sessions)

13:00-14:30 John Sekar, Robert Sheehan, and Jose Juan Tapia, University of Pittsburgh, Modeling Complex Biochemical Systems in Time and Space Using BioNetGen and MCell) (slides & materials)

13:00-14:30 William Mather, Virginia Tech, COPASI for Biochemical Network Simulation

13:00-14:30 OPEN

Break - 14:30-14:45

Session 1B - 14:45-16:15 (3 parallel sessions)

14:45-16:15 Steven S. Andrews, Fred Hutchinson Cancer Research Center, Smoldyn: Spatial Cell Biology Simulation

14:45-16:15 Emek Demir, Memorial Sloan Kettering Cancer Center, Pathway Commons/BioPAX

14:45-16:15 Ilya Nemenman, Emory University, Information Theory for Cells

Break - 16:15-16:30

Session 1C - 16:30-18:00 (2 parallel sessions)

16:30-18:00 Michael Blinov, University of Connecticut Health Center, VCell: Spatial Modeling, Reactions, and Rules

16:30-18:00 Alexander L. R. Lubbock and Oscar O. Ortega, Vanderbilt University, PySB, a programming environment to generate algorithmic representations of biological systems

Shuttle service will be available from 17:00-22:00.

Session 2: Opening Banquet (18:30 - 20:30, The Inn at Virginia Tech)

18:30-18:35 Welcome to q-bio, Will Mather, Virginia Tech

18:35-18:45 Viva q-bio! Jim Faeder, University of Pittsburgh

18:45-18:50 q-bio Summer School Recap, Brian Munsky, Colorado State University

18:50-18:55 q-bio Special Issue, Ilya Nemenman, Emory University

18:55-19:30 Dinner

19:30-19:35 Banquet Speaker Introduction, Jianhua Xing

19:35-20:30, John Tyson, Virginia Tech, Network Dynamics and Cell Physiology

Shuttle service will be available from 17:00-22:00.

Thursday, August 6

7:30-9:00 Breakfast (on own or Dietrick Dining Hall)

Shuttle service will be available from 8:00-10:00.

Registration (8:00 - 10:00, Squires Student Center)

Morning registration is available at the Squires Student Center. If you register after this time, information and a VT representative will be available at a table in the Squires Student Center.

Session 3 (9:00-12:20, Squires Student Center, Colonial Hall)

Chair: James Faeder, University of Pittsburgh

9:00-9:30 Johan Elf, Uppsala University, SMeagol Simulated Microscopy - a tool against inverse crimes

9:30-9:50 Andre Leier, Okinawa Institute of Science and Technology, Hierarchical membrane compartmentalization stabilizes IFN receptor dynamics

9:50-10:20 Hang Lu, Georgia Tech, Automation and Microfluidic Tools for Q-Bio

10:20-10:50 Coffee Break

10:50-11:10 Poster Spotlights 1

Deborah Striegel, NIH, Morphology of Pancreatic Islet Cytoarchitecture with Type 2 Diabetes

Jae Kyoung Kim, Ohio State, Determining the validity of Hill functions in stochastic simulations

Ryan Nikin-Beers, Virginia Tech, The role of antibody in dengue viral infection

Ji Hyun Bak, Princeton, Characterizing the statistical properties of protein surfaces

11:10-11:40 Oskar Hallatschek, UC Berkeley, Microbes Under Pressure

11:40-12:00 Lily Chylek, Cornell, IgE receptor signaling encodes dynamic memories of antigen exposure

12:00-12:20 Ryan Suderman, University of Kansas, The Noise is the Signal: Information Flow in Single Cells and Cellular Populations

12:20-14:30 Lunch (Dietrick Dining Hall)

Session 4 (14:30-17:30, Squires Student Center, Colonial Hall)

Chair: William Mather, Virginia Tech

14:30-15:00 Alejandro Colman-Lerner, University of Buenos Aires, Use of information far from steady-state by signal transduction systems.

15:00-15:20 Thomas Ouldridge, Imperial College, On the connection between computational and biochemical measurement

15:20-15:40 Jeremy Purvis, UNC-Chapel Hill, Single-cell dynamics reflect underlying signaling mechanisms

15:40-16:10 Coffee Break

16:10-16:30 Poster Spotlights 2

Abed Alnaif, UC Irvine, Pattern formation and morphogen gradients: A causality dilemma

Rory Donovan, University of Pittsburgh, Enhanced Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

Mark Transtrum, BYU, Effective models of emergent behavior from the manifold boundary approximation method

Vipul Periwal, NIH, The Universality of Cancer

16:30-16:50 Vernita Gordon, UT-Austin, The bacterial population’s spatial structure non-monotonically impacts bacterial growth

16:50-17:10 Nicholas C. Butzin, Virginia Tech, Entrainment of synthetic gene oscillators by a noisy stimulus

17:10-17:30 Arolyn Conwill, MIT, Seasonality gives rise to population oscillations in a bacterial cross-protection mutualism

Session 5 (19:00-20:00, Squires Student Center, Colonial Hall)

19:00-19:30 Sudhakaran Prabakaran, Science Signaling, How to Get Published in a Science Journal (slides)

19:30-20:00 Craig Giroux, NIH, Update on NIH Peer Review and Research Initiatives for Quantitative Biologists

Session 6 (20:00-23:00, Poster Session 1, Squires Student Center, Commonwealth Ballroom)

Official poster setup begins at 17:00, but poster boards may be ready by 12:00.

20:00-23:00 Poster Session 1 (snacks and drinks served)

Shuttle service will be available from 22:00-24:00.

Friday, August 7

7:30-9:00 Breakfast (on own or Dietrick Dining Hall)

Shuttle service will be available from 8:00-10:00.

Registration (Squires Student Center)

Information and a VT representative will be available at a table in the Squires Student Center.

Session 7 (9:00-12:20, Squires Student Center, Colonial Hall)

Chair: Yi Jiang, Georgia State

9:00-9:30 Arup Chakraborty, MIT, How to hit HIV where it hurts

9:30-9:50 Robin Lee, University of Pittsburgh, Cell fate decisions in response to a short pulse of TNF

9:50-10:20 John Hancock, UT Health Center, Ras nanoclusters: lipid-based assemblies for signal processing

10:20-10:50 Coffee Break

10:50-11:10 Poster Spotlights 3

Philip Hochendoner, Virginia Tech, Queueing Entrainment – Downstream control of a synthetic oscillator

Sargis Karapetyan, Duke, Redox rhythms reinforce the plant circadian clock: New insights into coupled biological oscillators

Xiuxiu He, Georgia State, How Adhesion Regulates Cell Migration Plasticity: A Computational Study

David Wooten, Vanderbilt, Transcription factor network supports phenotypic heterogeneity in cancer

11:10-11:40 Tamar Schlick, NYU, Simulating Large-Scale Chromatin Fibers

11:40-12:00 Allison Lopatkin, Duke, Microbial growth dynamics govern conjugation efficiency in the presence of antibiotics

12:00-12:20 Xiling Shen, Cornell, MicroRNA and protein cell fate determinants synergize in asymmetric division as safeguard against stem cell proliferation

12:20-14:30 Lunch (Dietrick Dining Hall)

Session 8 (14:30-17:20, Squires Student Center, Colonial Hall)

Chair: Orna Resnekov, Molecular Sciences Institute

14:30-15:00 Martin Howard, John Innes Center, How to control the size of a fission yeast cell

15:00-15:20 Robert Sheehan, University of Pittsburgh, Novel positive feedback loop sets antigen dose-dependent threshold for T cell differentiation

15:20-15:40 Megan McClean, University of Wisconsin, Robust network structure of the Sln1-Ypd1-Ssk1 three-component phosphorelay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae

15:40-16:10 Coffee Break

16:10-16:30 Poster Spotlights 4

Byoungkoo Lee, Georgia State, Cancer cell invasion analysis in ECM using in vitro models

Xiao-jun Tian, University of Pittsburgh, Molecular Cooperativity Leads to Monoallelic Olfactory Receptor Expression

Faisal Reza, Yale, Modeling Genomic Recombination Potentials Regulated by Synthetic Donor DNA and Triplex-forming Molecules

Fei Li, Virginia Tech, Stochastic Model of the Histidine Kinase Switch in the Caulobacter Cell Cycle

16:30-17:00 Li Zhaoping, UCL, A theory of the primary visual cortex, its zero-parameter quantitative prediction, and its experimental tests

17:00-17:20 Xiao Wang, Arizona State, Quorum-sensing crosstalk driven synthetic circuits: from unimodality to trimodality

Session 9 (19:00-20:00, Squires Student Center, Colonial Hall)

19:00-20:00 Special session, Paul Cohen, DARPA, Machines that Assemble Signaling Pathways by Reading the Literature: Progress in DARPA's Big Mechanism Program

Session 10 (20:00-23:00, Poster Session 2, Squires Student Center, Commonwealth Ballroom)

Official poster setup begins at 17:00, but feel free to setup starting around 8:30.

20:00-23:00 Poster Session 2 (snacks and drinks served)

Shuttle service will be available from 22:00-24:00.

Saturday, August 8

7:30-9:00 Breakfast (on own or Dietrick Dining Hall)

Shuttle service will be available from 8:00-10:00.

Registration (Squires Student Center)

Information and a VT representative will be available at a table in the Squires Student Center.

Session 11 (9:00-12:30, Squires Student Center, Colonial Hall)

Chair: Yang Cao, Virginia Tech

9:00-9:30 Karsten Weis, ETH, Global Changes In Chromosome Conformation In Budding Yeast In Different Physiological Conditions

9:30-9:50 Ilya Nemenman, Emory, Sensing Multiple Ligands with a Single Receptor

9:50-10:10 Eric Batchelor, NCI, Functional Roles of p53 Dynamics in Regulating Target Gene Expression

10:10-10:30 David Bruce Borenstein, Princeton, Established microbial colonies can survive Type VI secretion assault

10:30-11:00 Coffee Break

11:00-11:30 Linda Broadbelt, Northwestern, Discovery and Analysis of Novel Biochemical Transformations

11:30-11:50 Rhys Adams, ENS, Measuring the sequence-affinity landscape of antibodies

11:50-12:10 Heungwon Park, Duke, A synthetic oscillator couples to the cell division cycle in budding yeast

12:10-12:30 David Fange, Uppsala, Growth rate variations establish distributions of generation times and division sizes in E. coli

12:30-14:30 Lunch

Session 12 (14:30-18:00, Squires Student Center, Colonial Hall)

Chair: John Tyson, Virginia Tech

14:30-15:00 Carla Finkielstein, Virginia Tech, A systems-driven experimental approach reveals the complex regulatory distribution of p53 by circadian factors

15:00-15:20 Daniel Lewis, UC Davis, Unraveling dynamics of reconfigurable network motifs using a synthetic biology approach

15:20-15:40 Alan L. Hutchison, University of Chicago, Stochastic modeling of variability in circadian rhythms utilizing measured variance

15:40-16:00 Ertugrul Ozbudak, Albert Einstein, Stochasticity and the Mechanism of Precision in the Vertebrate Segmentation Clock

16:00-16:30 Coffee Break

16:30-17:00 Jeff Hasty, UCSD, Engineered Gene Circuits: From Clocks and Biopixels to Stealth Delivery

17:00-17:20 Neil Adames, Virginia Tech, Testing predictions of a new model for the budding yeast START transition using novel cell cycle mutants

17:20-17:40 Tatiana Marquez-Lago, Okinawa Institute of Science and Technology, Cell-cycle synchronized oscillations of a negatively self-regulated gene in E. coli

17:40-18:00 Erel Levine, Harvard, Coordinated heat-shock response in C. elegans

Shuttle service will be available from 17:00-22:00.

Session 13: Closing Banquet (18:30-20:45, The Inn at Virginia Tech)

18:30-18:35 Acknowledgments, Will Mather, Virginia Tech

18:35-18:40 q-bio Special Issue, Ilya Nemenman, Emory

18:45-18:50 q-bio 2016: Next year in Nashville, Erin Rericha, Vanderbilt

18:30-19:45 Dinner

19:45-19:50 Banquet Speaker Introduction, David Schwab, Northwestern

19:50-20:45 Phil Nelson, University of Pennsylvania, Old and new news about single-photon sensitivity in human vision

Shuttle service will be available from 17:00-22:00.

Acknowledgement of Funding

We would also like to thank contributions from the NM Spatiotemporal Modeling Center (through the balance of money they provided last year to NMC for q-bio 2014).