2015 q-bio Schedule (CSU)

Below we will place the schedule of the 2015 q-bio Summer School as it begins to evolve. Please keep in mind that this is subject to change up to the last minute.

Description of events:

General Seminars, Keynote Presentations, and Invited Talks- These are traditional seminar style presentations. These are open and available to the public. Many of these will be video-recorded and later posted online.

Chalk Talks - This is a more in-depth discussion or pedagogical lecture on a topic. These are open to registered participants or with consent from the organizers. A select few of these will be video-recorded and later posted online.

Breakout Sessions - These are more tutorials or software demonstrations. These are open to registered participants or with consent from the organizers.

Student Talks - These are 15 minute student presentations. These are open to registered participants and to the public with consent of each presenter.

Week 1, July 5-10, 2015

Sunday, July 5, 2015

17:00-20:00 Welcome reception

Monday, July 6, 2015

08:10-08:30 Introduction to the 2015 q-bio Summer School, Scott Building, Room 101
- 08:10-08:20 Welcome and Introduction to q-bio, Brian Munsky, Chemical and Biological Engineering, Colorado State University
- 08:20-08:30 Welcome and Introduction to CSU, Rick Miranda, Provost and Executive Vice President, Colorado State University
08:30-09:20 General Seminar 1, Brian Munsky, Colorado State University, "Introduction to Stochastic Gene Regulation", Scott Building, Room 101
09:30-10:20 General Seminar 2, Marek Kimmel, Rice University, "TCGA Data and Models of Cancer Evolution", Scott Building, Room 101
10:30-11:20 General Seminar 3, Ashok Prasad, Colorado State University, "Introduction to Complex Biological Dynamics", Scott Building, Room 101
11:30-13:15 Lunch
13:30-14:45 Chalk Talk - David Axelrod, Rutgers University, "Pathobiology of Cancer I", Scott Building, Room 229, Stream Video
15:00-16:15 Breakout Session 1, Douglas Shepherd, University of Colorado at Denver, "Writing and running the Gillespie stochastic simulation algorithm", Scott Building, Room 229, Stream video
16:30-17:45 General Seminar 4, William Hlavacek, Los Alamos National Laboratory, "Introduction to rule-based modeling", Scott Building, Room 229, Stream video
18:00-20:00 Opening Poster Session, Scott Building Atrium (drinks and hors d'oeuvres will be served).

Tuesday, July 7, 2015

08:30-09:30 General Seminar 5, Douglas Shepherd, University of Colorado at Denver, "Single-Molecule approaches in Quantitative Biology", Scott Building, Room 229, Stream video
09:30-10:00 Coffee Break and Panel Discussion
10:15-11:30 Student Talks 1-4, Scott Building, Room 101
- 1 Ania Baetica, California Institute of Technology, A stochastic framework for the design of transient and steady state behavior of biochemical reaction networks, Scott Building, Room 101
- 2 Wenlong Xu, Colorado State University, A Mathematic Minimal Model for Proximity Substrate Channeling in Bifunctional Enzyme, Scott Building, Room 101
- 3 Pu Han, Rice University, Coevolution of CRISPR bacteria and phages, Scott Building, Room 101
- 4 Marcal Gabalda, Pompeu Fabra University (Spain), Long-range synchronized oscillations in biofilm as a mechanism to compensate colony growth and resilience, Scott Building, Room 101
11:30-13:00 Lunch
13:30-14:45 General Seminar 6, Sabrina Spencer, University of Colorado at Boulder, "Single-cell dynamics of cell-cycle commitment", Scott Building, Room 229.
15:00-16:15 Breakout Session 2, David Axelrod, Rutgers University, "Pathobiology of Cancer II", Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 3, William Hlavacek, Los Alamos National Laboratory, "Rule-based modeling with the RuleBender/BioNetGen/NFsim software stack", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
19:30-21:30 Special Contributed Evening Session, Robert Sidney Cox, Kobe University (Japan), "Statistical mechanics of repression", Scott Building, Room 229

Wednesday, July 8, 2015

08:30-09:30 General Seminar 7, David Axelrod, Rutgers University, "Breast Cancer – Deterministic Modeling of Tumor Progression Based Upon Clinical Histopathology Data", Scott Building, Room 229, Stream video
09:30-10:00 Coffee Break and Panel Discussion
10:15-11:30 Student Talks 5-8, Scott Building, Room 101
- 5 Sarah Kaspar, University of Heidelberg (Germany), Biological information processing from intracellular calcium to target proteins, Scott Building, Room 101
- 6 Tony Szedlak, Michigan State University, Many-attractor signaling dynamics in complex biological networks, Scott Building, Room 101
- 7 Kevin Hoover, University of Colorado at Denver, Detecting Change in a Noisy World, Scott Building, Room 101
- 8 Robert Johnson, Imperial College London (England), Noise decomposition: intrinsic and extrinsic noise, reaction by reaction, Scott Building, Room 101
11:30-13:15 Lunch
13:30-14:45 General Seminar 8, Lev Tsimring, University of California at San Diego, Scott Building, Room 229, Stream video
15:00-16:15 Breakout Session 4(Chalk talk), Marek Kimmel, Rice University, Introduction, Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 5, Brian Munsky, Colorado State University, "Using the Finite State Projection Algorithm, Part 1", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
20:00-21:30 Special Evening Session Cancer Dynamics, David Axelrod, Rutgers University, "Colon Cancer – Stochastic Modeling of Stem Cell Dynamics to Improve Treatment and Prevention", Scott Building, Room 229
20:00-21:30 Special Contributed Evening Session, David Priest, RIKEN QBIC (Osaka, Japan), "Quantitative characterization of long distance looping", Scott Building, Room 101

Thursday, July 9, 2015

08:30-09:30 General Seminar 9, Patrick Shipman, Colorado State University, Scott Building, Room 229, Stream video
09:30-10:00 Coffee Break and Panel Discussion
10:15-11:30 Student Talks 9-12, Scott Building, Room 101
- 9 Peter Czuppon, University of Freiburg (Germany), Classification of phenotypic subpopulations in isogenic bacterial cultures, Scott Building, Room 101
- 10 Katharine Schaumberg, Colorado State University, Building a Genetic Toggle Switch in Plants, Scott Building, Room 101
- 11 Monica Garcia, Institute of Ecology, National Autonomous University of Mexico, Mechanistic model links tissue patterning with the specificity of auxin responses in the Arabidopsis root stem cell niche, Scott Building, Room 101
- 12 Roman Jaksik, Silesian University of Technology (Poland), Study of cellular viability control using Solvary application, Scott Building, Room 101
11:30-13:15 Lunch
13:30-14:45 Chalk talk, Jaroslaw Smieja, Sileasian University of Technology (Poland), "Models of cancer dynamics with control actions", Scott Building, Room 229, Stream video
15:00-16:15 General Seminar 10, Xuedong Liu, University of Colorado at Boulder, "Systems biology of autocrine signaling during epithelial sheet migration", Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 6, Ashok Prasad, Colorado State University, "Overview of Dynamical Systems: Stability and Bifurcations", Scott Building, Room 229, Stream video (no sound)
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
20:00-21:30 Special Evening Session for Cancer Dynamics, Roman Jaksik, Silesian University of Technology, "Cancer genomes in the TCGA database: Introduction and hands-on practice session", Scott Building, Room 229

Friday, July 10, 2015

08:30-09:30 General Seminar 11, Jaroslaw Smieja, Sileasian University of Technology (Poland), "Anticcancer therapy as an optimization problem", Scott Building, Room 229, Stream video
09:30-10:00 Coffee Break and Panel Discussion
10:15-11:30 Breakout Session 7, Simon Taverner, "Sensitivity Analyses", Scott Building, Room 101, Stream video
11:30-13:15 Lunch
13:30-14:45 Chalk talk - Patrick Shipman, Colorado State University, "Overview of Dynamical Systems: Oscillations and Excitability", Scott Building, Room 229, Stream video (partial board only)
15:00-16:15 Breakout Session 8, Rosemary Braun, Northwestern University, "Identifying aberrant network dynamics in cancer", Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 9, Douglas Shepherd, University of Colorado at Denver, "Modeling and Interpreting Single-Molecule Experiments", Scott Building, Room 229
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)

Weekend, July 11-12, 2015

Saturday afternoon, New Belgium Brewery tour.

Week 2, July 13-17, 2015

Monday, July 13, 2015

08:30-09:30 General Seminar 12, Eli Shlizerman, University of Washington, Scott Building, Room 229, Stream video
10:00-10:30 Coffee Break and Panel Discussion
10:15-11:30 Project time.
11:30-13:15 Lunch
13:30-14:45 Chalk talk - Eli Shlizerman, University of Washington, Scott Building, Room 229
15:00-16:15 Breakout Session 10/Chalk talk, Marek Kimmel, Rice University, Stochastic processes in cancer modeling, Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 11, Douglas Shepherd, University of Colorado at Denver, "Tutorial on Single-Molecule Data Analysis", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
20:00-21:30 Special evening session for Cancer Dynamics, Marek Kimmel, Rice University, "Additional math models of cancer and some math proofs", Scott Building, Room 229

Tuesday, July 14, 2015

08:30-09:30 General Seminar 13, Seth Corey, Northwestern University, Scott Building, Room 229, Stream video
09:45-10:30 Coffee Break and Panel Discussion, Forming collaborations between experimentalists and theorists, (S. Corey, D. Shepherd, A. Ben-Hur, S. Tobet) Scott Building, Room 101
10:30-11:45 Student Talks 13-16, Scott Building, Room 101
- 13 Eline Vetters, University of Leuven (Belgium), Particle-based modeling of crucial signaling pathways influencing hematopoietic stem cell behavior in mouse fetal liver, Scott Building, Room 101
- 14 Michael Trogdon, University of California at Santa Barbara, Simulating Yeast Polarization in the Cloud, Scott Building, Room 101
- 15 Zach Fox, Colorado State University, Using Noise in Gene Expression to Fit and Predict Single-cell RNA Distributions, Scott Building, Room 101
- 16 Dinh Khahn, University of Alabama at Tuscaloosa, Analysis of Inexact Krylov Subspace Approximation to the Matrix Exponential, Scott Building, Room 101
11:30-13:15 Lunch
13:30-14:45 Chalk talk - Bard Ermentrout, University of Pittsburgh, XPP-Aut for Neurons, Scott Building, Room 229, Stream video
15:00-16:15 Breakout Session 12, Seth Corey, Stream video
16:30-17:45 Breakout Session 13, Jaroslaw Smieja, Sileasian University of Technology (Poland), "Control optimization - mathematical background", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
20:00-21:30 Special Evening Session for Single-Molecule Data Analysis, Douglas Shepherd, University of Colorado at Denver, Scott Building, Room 229

Wednesday, July 15, 2015

08:30-09:30 General Seminar 14, Bard Ermentrout, University of Pittsburgh, "Fields of Dreams -- Modeling and analysis of large scale activity in the brain", Scott Building, Room 229, Stream video
09:45-10:30 Photos and Coffee Break
10:30-11:45 Student Talks 17-20, Scott Building, Room 101
- 17 Tomasz Jetka, Institute of Fundamental Technological Research, Polish Academy of Science, Measuring information transmission from single-cell heterogenous dynamical responses, Scott Building, Room 101
- 18 Huy Vo, University of Alabama at Tuscaloosa, Variants of the Krylov-based Finite State Projection algorithm for solving the Chemical Master Equation, Scott Building, Room 101
- 19 Ralf Schmidt, Universität Basel (Switzerland), Mapping the dynamics of mRNA polyadenylation in mammalian cells, Scott Building, Room 101
- 20 Zach Sethna, Princeton University, Statistical Inference of the Immune System Repertoire Scott Building, Room 101
11:30-13:15 Lunch
13:30-14:45 Chalk talk - Abhyudai Singh, University of Delaware, "Using Moment Generating Functions", Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 15/Chalk talk, Rosemary Braun, Northwestern University, "Network analysis of genomic data", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
20:00-21:30 Special Evening Session for Cancer Dynamics, Jaroslaw Smieja, Sileasian University of Technology (Poland),"Modeling in understanding intracellular processes activated by anticancer agents and stress factors", Scott Building, Room 229

Thursday, July 16, 2015

08:30-09:30 General Seminar 15, Abhyudai Singh, University of Delaware, "Modeling bacteriophage lambda lysis time through first-passage time calculations", Scott Building, Room 229, Stream video
09:45-10:30 Coffee Break and Panel Discussion, Finding a new postdoc or faculty position, (A. Singh, S. Ho, D. Shepherd, R. Braun, S. Presse), Scott Building, Room 101
10:30-11:45 Student Talks 21-24, Scott Building, Room 101
- 21 Amy Chang, University of California at San Francisco, Characterizing Population-level Heterogeneities in Mammalian Organelle Morphology, Scott Building, Room 101
- 22 Robert Amezquita, Yale University, Transcriptional and Epigenetic Networks Driving CD8+ T Cell Differentiation, Scott Building, Room 101
- 23 Omer Karin, Weizmann Institute Of Science (Israel), Glucose Homeostasis can be Maintained by a Direct Effect on Beta Cell Apoptosis, Scott Building, Room 101
- 24 Open, Scott Building, Room 101
11:30-13:15 Lunch
13:30-14:45 Chalk talk, Steve Presse, Indiana University and Purdue University, "Model selection and MaxEnt I", Scott Building, Room 229, Stream video
15:00-16:15 Breakout Session 15 - Marek Kimmel, Rice University, Stochastic models of proliferation and mutation in cancer, Scott Building, Room 229, Stream video
16:30-17:45 Chalk talk, Steve Presse, Indiana University and Purdue University, "Model selection and MaxEnt II", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)
20:00-21:30 Special Evening Session for Cancer Dynamics, Mohit Kumar Jolly, Rice University, Clusters of Circulating Tumor Cells: the primary ‘bad agents’ of metastasis, Scott Building, Room 229

Friday, July 17, 2015

08:30-09:30 General Seminar 16, Steve Presse, Indiana University and Purdue University, "Inferring Models of Biophysical Dynamics from Imaging and Spectroscopy Data", Scott Building, Room 229, Stream video
09:45-10:30 Coffee Break and Panel Discussion, Navigating the tenure and promotion process, (A. Prasad, P. Shipman, A. Ben-Hur, S. Tobet), Scott Building, Room 101
10:30-11:30 Project time.
11:30-13:15 Lunch
13:30-14:45 Chalk talk - Abhyudai Singh, University of Delaware, "Computing Moment Dynamics", Scott Building, Room 229, Stream video
15:00-16:15 Breakout Session 17, Patrick Shipman, Colorado State University, "Data Analysis", Scott Building, Room 229, Stream video
16:30-17:45 Breakout Session 18, Jaroslaw Smieja, Sileasian University of Technology (Poland), "Infinite-dimensional models and their analysis", Scott Building, Room 229, Stream video
18:00-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)

Week 3, July 20-21, 2015

Monday, July 20, 2015

All Presentations Scott Building, Room 101.

09:30 - 09:40 Project Presentation 2 - Elaheh Alizadeh (with Jaroslaw Smieja)
09:40 - 10:00 Project Presentation 3 - Siyi Chen, Roman Jaksik (with Marek Kimmel)
10:00 - 10:20 Project Presentation 4 - Khanh Dinh, Katherine Schaumberg (with Marek Kimmel)
10:45 - 11:45 Panel Discussion -- "Postdoc Fellowships and Opportunities and How to Find Them," (D. Bush, R. Braun, G. Peers, C. Wilusz, J. Moreno), Resources for students seeking postdocs
11:45 - 13:30 Lunch
12:00 - 13:20 Lunch Group Discussion -- "Women in Science Careers" (R. Braun, C. Menoni, C. Wilusz)
13:30 - 14:10 Project Presentation 5 - Robert Amezquita, Tomasz Jetka, Chintan Joshi, Omer Karin, Ralf Schmidt, and Katie Lee (with Rosemary Braun)
14:10 - 14:40 Project Presentation 6 - Peter Czuppon, Zach Fox, Pu Han, Robert Johnson, Ben Kessler, Michael May, Om Patange, Marcal GabaldÃ Sagarra (with Brian Munsky)
14:40 - 15:10 Project Presentation 7 - Monica Garcia Gomez, Sarah Luck, Anthony Szedlak, Ali, Michael Trogdon (with Ashok Prasad)
15:10 - 15:40 Project Presentation 8 - Ania Baetica, Zach Fox, Michael May, Huy Vo (with Brian Munsky)
15:40 - 15:50 Farewell Discussion -- "The Future of q-bio in Colorado and Abroad"
17:30-19:15 Dinner Break (Note: Dining Commons Stop Serving Dinner at 18:30pm)

Tuesday, July 21, 2015

The First Annual Front Range Computational Biology Symposium