The Fifth q-bio Conference on Cellular Information Processing

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Back to The Fifth q-bio Conference.

The q-bio Conference is intended to advance predictive modeling of cellular regulation. The emphasis is on modeling and quantitative experimentation for understanding and predicting the behaviors of particular regulatory systems, phenomena that manifest themselves in many biological systems, and/or general principles of cellular information processing.

The single-track program will include invited talks from leading experimental and theoretical researchers (confirmed speakers are listed below), as well as contributed talks, poster presentations, and tutorials selected from abstract submissions. The program includes two banquets, tutorials, multiple sessions covering a range of topics, and two evening poster sessions.

Lodging is available for participants at the conference venue, facilitating interactions and stimulating informal discussions of quantitative biology. Space is available for 200 participants. If registration demand exceeds capacity, preference will be given to individuals selected to make presentations at the meeting.

The q-bio Summer School will precede the conference. It will take place in Los Alamos- students will then attend the q-bio Conference. The school is intended for researchers new to modeling cellular regulatory systems. Scholarships are available. Travel awards are also available to help graduate students and postdocs attend the conference. Apply for admission to the summer school and/or financial support by submitting a CV along with an abstract for a contributed talk or poster presentation at the conference.

Please visit the new conference website at:

The q-bio Conference is not affiliated with arXiv.q-bio, but symbiotically coordinates with it.


Call For Abstracts

Abstracts are now being accepted. To view the call for abstracts, please click here: Call for Abstracts


For more information about the 2011 q-bio Conference, please feel free to contact the organizers ( We would be delighted to help you with any special needs (e.g., finding family care in Santa Fe).

Important Dates

The Fifth Annual q-bio Conference is scheduled for August 10-13, 2011 with satellite workshops on August 14, 2011. The Fifth Annual q-bio Summer School is scheduled for July 25-August 9, 2011.

  • Satellite Workshop Proposals: December 10, 2010
  • Tutorial Proposals: January 19, 2011
  • Summer School Applications: February 25, 2011
  • Abstract Submission Deadline: Extended to April 22, 2011
  • Early Registration Opens: May 20, 2011. To Register, please Click Here.
  • Early Registration Closes: June 20, 2011


Detailed Program

WednesdayAugust 10, 2011
12:00-17:00Tutorial Session, Classrooms (check registration desk)
12:00-14:00Steven Gross, University of California, Irvine, From single motors to ensemble function: What is important for how motors work together?
12:00-13:30James Faeder, University of Pittsburgh School of Medicine, Rule-based modeling with BioNetGen
14:00-17:00James Glazier, Indiana University, Developing multi-cell developmental and biomedical simulations using CompuCell3D
14:00-17:00Ilya Nemenman , Emory University, Information processing in cell biology
14:00-17:00Tudor Oprea, Gergely Zahoransky-Kohalmi, and Jeremy Yang, University of New Mexico, Network-based analyses of drugs, targets, and clinical outcomes
14:00-17:00Avi Ma'ayan, Mount Sinai School of Medicine, Icahn Medical Institute, Tutorial: Network analysis and gene-list enrichment analysis in systems biology
15:00-17:00Brian Munsky and Gregor Neuert, Los Alamos National Laboratory and MIT, Identifying stochastic models using flow cytometry and fluorescence microscopy
17:30-20:00Opening Banquet, Great Hall
17:30-17:45Welcome Comments from Organizers and LANL Administration
17:45-17:50Summer School Recap, Brian Munsky, Los Alamos National Laboratory
19:00-19:05Banquet Speaker Introduction, Ilya Nemenman , Emory University
19:05-20:00Opening Banquet Talk, Dennis Bray, University of Cambridge, Protein Computations and the Origins of Behavior
ThursdayAugust 11, 2011
7:30-8:30Breakfast, Dining Hall (service 7:30-9:30)
8:30-12:15Session I, Great Hall, Chair: Yi Jiang, Los Alamos National Laboratory
8:30-9:00Uri Alon, Weizmann Institute, Design principles of Biological Circuits
9:00-9:20Tom Shimizu, FOM Institute AMOLF, Response rescaling in bacterial chemotaxis
9:20-9:40Sriram Chandrasekaran, University of Illinois, Urbana-Champaign, Brain Transcriptional Regulatory Network Quantitatively Predicts Behavior-Specific Gene Expression
9:40-10:00Gregor Neuert, Massachusetts Institute of Technology, Systematic Identification of Signal-Activated Stochastic Gene Regulation
10:00-10:30Coffee Break
10:30-10:45Poster Spotlights I
Emily Capra, Massachusetts Institute of Technology, Evolution of two-component signaling systems
Xianrui Cheng, Duke University, Autonomous Boolean models reveal timing constraints on embryonic developmental pattern formation
Lily Chylek, Cornell University, Interaction libraries for rule-based modeling
10:45-11:15Pieter Rein ten Wolde, FOM Institute AMOLF, Single-cell ultrasensitivity and stochasticity give rise to bimodal response on the population level
11:15-11:35Fang Huang, University of New Mexico, Fast, simultaneous multiple-emitter fitting for single molecule super-resolution imaging
11:35-11:55Lei Dai, Massachusetts Institute of Technology, Experimental Observation of Early Warning Signals for Approaching Population Collapse
11:55-12:15Xiling Shen , Cornell University, Asymmetric Cell Fate Decisions in Colon Cancer Stem Cells
12:15-14:30Lunch, Dining Hall (service 11:30-13:30)
14:30-18:25Session II, Great Hall, Chair: James Fader, University of Pittsburgh School of Medicine
14:30-15:10Pioneer Talk, Nadrian Seeman, New York University, DNA: Not Merely the Secret of Life
15:10-15:30Oleg Igoshin, Rice University, Self-organization mechanisms in Myxococcus xanthus swarms
15:30-15:50Robert Egbert , University of Washington, Tuning Gene Networks with Simple Sequence Repeats
15:50-16:10Kevin Wood, Harvard University, Using Maximum Entropy to Decode the Multi-drug Response in Bacteria
16:10-16:40Coffee Break
16:40-16:55Poster Spotlights II
John Kang, Carnegie Mellon University, Coarse-grained Modeling of Actin Cytoskeletal Alignment to Mechanical Stimulation
Eric Batchelor, Harvard Medical School , Stimulus-dependent dynamics of p53 in single cells
Eugene Yurtsev, Massachusetts Institute of Technology, Microbial Cheating Limits the Evolution of Antibiotic Resistance
16:55-17:25Diane Lidke, University of New Mexico, Measuring Membrane Receptor Interactions Using Single Quantum Dot Tracking
17:25-17:45Eric Deeds, The University of Kansas, Optimizing ring assembly: the strength of weak bonds
17:45-18:05Can Guven, University of Maryland, Stability Analysis of a Model for Collective Migration of Dictyostelium Discoideum
18:05-18:25Maciej Dobrzynski, Systems Biology Ireland, University College Dublin, Single-cell ultrasensitivity and stochasticity give rise to bimodal response on the population level
18:25-20:30Dinner in town , (no meal service at St. John's)
20:30-23:30Poster Session I ( [_blank q-Bio-Poster-Set-1b] )
FridayAugust 12, 2011
7:30-8:30Breakfast, Dining Hall (service 7:30-9:30)
8:30-12:15Session III, Great Hall, Chair: William Hlavacek, Los Alamos National Laboratory and Translational Genomics Research Institute
8:30-9:00Reka Albert, Pennsylvania State University, Discrete dynamic modeling of signal transduction networks
9:00-9:20David Klinke , West Virginia University, Quantifying cross-talk among Interferon-γ, Interleukin-12 and Tumor Necrosis Factor signaling pathways within a TH1 cell model: A model-based inference approach
9:20-9:40Mohammad Fallahi-Sichani, University of Michigan, The dynamics of TNF signaling control tuberculosis granuloma formation
9:40-10:00Huilei Xu, Mount Sinai School of Medicine, Functional Atlas of Mouse Embryonic Stem Cells Pluripotency and Early Differentiation
10:00-10:30Coffee Break
10:30-10:45Poster Spotlights III
Jakub Otwinowski, Emory University, Speeding up evolutionary search by small fitness fluctuations
Christian Ray, University of Texas M. D. Anderson Cancer Center, Amelioration of ultrasensitive biochemical switches in bacteria
John Sekar, University of Pittsburgh, Experimental Design in Rule-Based Models
10:45-11:15Tobias Meyer, Stanford University, A two dimensional Akt-Erk signaling code for NGF-triggered differentiation and cell number expansion
11:15-11:35Edward Stites, Translational Genomics Research Institute, Promiscuity quantitatively and qualitatively impacts early growth factor receptor signaling
11:35-11:55Raymond Cheong, Johns Hopkins University, Advantages and limitations of network-based information processing in biological signaling systems
11:55-12:15Christopher Zopf, Massachusetts Institute of Technology, Single promoters as regulatory network motifs
12:15-14:30Lunch, Dining Hall (service 11:30-13:30)
14:30-18:15Session IV, Great Hall, Chair: Gnana Gnanakaran, Los Alamos National Laboratory
14:30-15:00Alan Perelson, Los Alamos National Laboratory, Multiscale Modeling of Hepatitis C Virus Infection
15:00-15:20Cheemeng Tan , Carnegie Mellon University, The inoculum effect and band-pass bacterial response to periodic antibiotic treatment
15:20-15:40Ni Ji, Massachusetts Institute of Technology, _Genetic redundancy in the Wnt pathway promotes robust control of neuronal migration through interlocked feedback loops
15:40-16:00Karina Mazzitello, Universidad Nacional de Mar del Plata, Modeling Morphology Dynamics of Retinal Pigment Epithelium
16:00-16:30Coffee Break
16:30-16:45Poster Spotlights IV
Rui Zhen Tan, Massachusetts Institute of Technology, Different roles of Wnt ligands and receptors in regulating C.elegans' cell divisions
Karen Tkach, Memorial Sloan Kettering Cancer Center, Regulation of T cell Antigen Dose-Dependent IL-2 Production via Population Dynamics
Cathy McKinney, Stowers Institute for Medical Research, Semi-Automated Analysis of Proliferation Dynamics of Human Metastatic Melanoma
16:45-17:15Michael Laub, Massachusetts Institute of Technology and Howard Hughes Medical Institute, Specificity and Evolution of Bacterial Signaling Pathways
17:15-17:35Howard Salis, Pennsylvania State University, Automated Design of Synthetic Bacterial Small RNAs
17:35-17:55Mark Maienschein-Cline, University of Chicago, Identification of transcription factor targets by analysis of high-throughput data
17:55-18:15Veronika Zarnitsyna, Georgia Institute of Technology, Kinetics of molecular interactions across the T cell – APC junction
18:30-20:00Dinner (service), Koi Pond
19:00-20:00Session V, Koi Pond, Chair: Michael Wall, Los Alamos National Laboratory
19:00-19:05Introduction on the Social Aspects of Science
19:05-20:00Guitar Session: Love and Fear in the Lab, Uri Alon, Weizmann Institute
20:00-23:00Poster Session II ( [_blank q-Bio-Poster-Set-2b] )
SaturdayAugust 13, 2011
7:30-9:10Breakfast, Dining Hall (service 7:30-9:30)
9:10-12:30Session VI, Great Hall, Chair: Brian Munsky, Los Alamos National Laboratory
9:10-9:40Nicole King, University of California, Berkeley, The origin of animal multicellularity
9:40-10:00Evgeni Nikolaev, Rutgers, The State University of New Jersey, Mathematical Modeling Describes a Novel Bistable Mechanism of Lipid Body Formation in Macrophages Infected with M. tuberculosis
10:00-10:20Rebecca McLennan, Stowers Institute for Medical Research, Elucidating multiscale mechanisms of neural crest migration
10:20-10:50Wallace Marshall, University of California, San Francisco, Biological Noise at the level of Cellular Structure
10:50-11:20Coffee Break
11:20-11:50Stas Shvartsman, Princeton University, Multiscale studies of embryonic development: experiments and theory
11:50-12:10Stephen Helms, University of Texas Southwestern Medical Center, A Tandem PDZ Domain Redox Switch in InaD
12:10-12:30Domitilla Del Vecchio, Massachusetts Institute of Technology, The Impact of Retroactivity on the Signal Processing of Transduction Networks
12:30-14:30Lunch, Dining Hall (service 11:30-13:30)
14:30-18:10Session VII, Great Hall, Chair: Ilya Nemenman, Emory University
14:30-15:00Alexander Hoffmann, University of California, San Diego, Parsimonious Gene Regulatory Network modeling reveals mRNA half-life control of the pathogen-responsive transcriptome
15:00-15:20Bernie Daigle, Jr., University of California, Santa Barbara, Accelerated Maximum Likelihood Estimation for Stochastic Biochemical Systems
15:20-15:40Alistair Boettiger, University of California, Berkeley, No Compromise: Single molecule imaging reveal mechanisms for speed and precision in developmental gene expression
15:40-16:10Vittorio Cristini, University of New Mexico, Tumor Modeling
16:10-16:40Coffee Break
16:40-17:10Michael Deem, Rice University, Heterogeneous Diversity of Spacers within CRISPR
17:10-17:30Qiong Yang, Stanford University, Switch-like negative feedback promotes clock-like mitotic oscillation
17:30-17:50Alexandra Jilkine, University of Arizona, A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules
17:50-18:10Wan-Chen Lin, University of California, Berkeley, Spatial organization in cell membranes
18:30-20:30Closing Banquet, Dining Hall
18:30-18:35Farewell, Michael Wall, Los Alamos National Laboratory
19:30-19:35Banquet Speaker Introduction, William Hlavacek, Los Alamos National Laboratory and Translational Genomics Research Institute
19:35-20:30Closing Banquet Talk, Peter Sorger, Harvard Medical School, Measuring and Modeling Cell Decision Processes
SundayAugust 14, 2011
9:00-17:00 Sunday Satellite: Second workshop on rule-based modeling of biochemical systems

q-bio Summer School

The q-bio Summer School is an affiliated event that precedes the conference. It is intended for investigators new to modeling of cellular regulatory systems.

Satellite Workshops

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