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The Fifth q-bio Conference on Cellular Information Processing
From Q-bio
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: http://guest.cvent.com/d/8dqhzx
The q-bio Conference is not affiliated with arXiv.q-bio, but symbiotically coordinates with it.
Contents
Call For Abstracts
Abstracts are now being accepted. To view the call for abstracts, please click here: Call for Abstracts
Contact
For more information about the 2011 q-bio Conference, please feel free to contact the organizers (q-bio11@cnls.lanl.gov). 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, 2010Tutorial Proposals: January 19, 2011Summer School Applications: February 25, 2011Abstract Submission Deadline: Extended to April 22, 2011- Early Registration Opens: May 20, 2011. To Register, please Click Here.
- Early Registration Closes: June 20, 2011
Participants
- Organizers
- Invited Speakers
- Contributed Speakers
- Tutorial Presenters
- Poster Spotlight Presenters
- Poster Presenters
- All Participants (alphabetical list)
Detailed Program
| Wednesday | August 10, 2011 |
| 12:00-17:00 | Tutorial Session, Classrooms (check registration desk) |
| 12:00-14:00 | Steven Gross, University of California, Irvine, From single motors to ensemble function: What is important for how motors work together? |
| 12:00-13:30 | James Faeder, University of Pittsburgh School of Medicine, Rule-based modeling with BioNetGen |
| 14:00-17:00 | James Glazier, Indiana University, Developing multi-cell developmental and biomedical simulations using CompuCell3D |
| 14:00-17:00 | Ilya Nemenman , Emory University, Information processing in cell biology |
| 14:00-17:00 | Tudor Oprea, Gergely Zahoransky-Kohalmi, and Jeremy Yang, University of New Mexico, Network-based analyses of drugs, targets, and clinical outcomes |
| 14:00-17:00 | Avi Ma'ayan, Mount Sinai School of Medicine, Icahn Medical Institute, Tutorial: Network analysis and gene-list enrichment analysis in systems biology |
| 15:00-17:00 | Brian Munsky and Gregor Neuert, Los Alamos National Laboratory and MIT, Identifying stochastic models using flow cytometry and fluorescence microscopy |
| 17:30-20:00 | Opening Banquet, Great Hall |
| 17:30-17:45 | Welcome Comments from Organizers and LANL Administration |
| 17:45-17:50 | Summer School Recap, Brian Munsky, Los Alamos National Laboratory |
| 17:50-19:00 | Dinner |
| 19:00-19:05 | Banquet Speaker Introduction, Ilya Nemenman , Emory University |
| 19:05-20:00 | Opening Banquet Talk, Dennis Bray, University of Cambridge, Protein Computations and the Origins of Behavior |
| Thursday | August 11, 2011 |
| 7:30-8:30 | Breakfast, Dining Hall (service 7:30-9:30) |
| 8:30-12:15 | Session I, Great Hall, Chair: Yi Jiang, Los Alamos National Laboratory |
| 8:30-9:00 | Uri Alon, Weizmann Institute, Design principles of Biological Circuits |
| 9:00-9:20 | Tom Shimizu, FOM Institute AMOLF, Response rescaling in bacterial chemotaxis |
| 9:20-9:40 | Sriram Chandrasekaran, University of Illinois, Urbana-Champaign, Brain Transcriptional Regulatory Network Quantitatively Predicts Behavior-Specific Gene Expression |
| 9:40-10:00 | Gregor Neuert, Massachusetts Institute of Technology, Systematic Identification of Signal-Activated Stochastic Gene Regulation |
| 10:00-10:30 | Coffee Break |
| 10:30-10:45 | Poster 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 | |
| 10:45-11:15 | Pieter Rein ten Wolde, FOM Institute AMOLF, Single-cell ultrasensitivity and stochasticity give rise to bimodal response on the population level |
| 11:15-11:35 | Fang Huang, University of New Mexico, Fast, simultaneous multiple-emitter fitting for single molecule super-resolution imaging |
| 11:35-11:55 | Lei Dai, Massachusetts Institute of Technology, Experimental Observation of Early Warning Signals for Approaching Population Collapse |
| 11:55-12:15 | Xiling Shen , Cornell University, Asymmetric Cell Fate Decisions in Colon Cancer Stem Cells |
| 12:15-14:30 | Lunch, Dining Hall (service 11:30-13:30) |
| 14:30-18:25 | Session II, Great Hall, Chair: James Fader, University of Pittsburgh School of Medicine |
| 14:30-15:10 | Pioneer Talk, Nadrian Seeman, New York University, DNA: Not Merely the Secret of Life |
| 15:10-15:30 | Oleg Igoshin, Rice University, Self-organization mechanisms in Myxococcus xanthus swarms |
| 15:30-15:50 | Robert Egbert , University of Washington, Tuning Gene Networks with Simple Sequence Repeats |
| 15:50-16:10 | Kevin Wood, Harvard University, Using Maximum Entropy to Decode the Multi-drug Response in Bacteria |
| 16:10-16:40 | Coffee Break |
| 16:40-16:55 | Poster 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 | |
| 16:55-17:25 | Diane Lidke, University of New Mexico, Measuring Membrane Receptor Interactions Using Single Quantum Dot Tracking |
| 17:25-17:45 | Eric Deeds, The University of Kansas, Optimizing ring assembly: the strength of weak bonds |
| 17:45-18:05 | Can Guven, University of Maryland, Stability Analysis of a Model for Collective Migration of Dictyostelium Discoideum |
| 18:05-18:25 | Maciej Dobrzynski, Systems Biology Ireland, University College Dublin, Single-cell ultrasensitivity and stochasticity give rise to bimodal response on the population level |
| 18:25-20:30 | Dinner in town , (no meal service at St. John's) |
| 20:30-23:30 | Poster Session I ( [_blank q-Bio-Poster-Set-1b] ) |
| Friday | August 12, 2011 |
| 7:30-8:30 | Breakfast, Dining Hall (service 7:30-9:30) |
| 8:30-12:15 | Session III, Great Hall, Chair: William Hlavacek, Los Alamos National Laboratory and Translational Genomics Research Institute |
| 8:30-9:00 | Reka Albert, Pennsylvania State University, Discrete dynamic modeling of signal transduction networks |
| 9:00-9:20 | David 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 |
| 9:20-9:40 | Mohammad Fallahi-Sichani, University of Michigan, The dynamics of TNF signaling control tuberculosis granuloma formation |
| 9:40-10:00 | Huilei Xu, Mount Sinai School of Medicine, Functional Atlas of Mouse Embryonic Stem Cells Pluripotency and Early Differentiation |
| 10:00-10:30 | Coffee Break |
| 10:30-10:45 | Poster 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 | |
| 10:45-11:15 | Tobias Meyer, Stanford University, A two dimensional Akt-Erk signaling code for NGF-triggered differentiation and cell number expansion |
| 11:15-11:35 | Edward Stites, Translational Genomics Research Institute, Promiscuity quantitatively and qualitatively impacts early growth factor receptor signaling |
| 11:35-11:55 | Raymond Cheong, Johns Hopkins University, Advantages and limitations of network-based information processing in biological signaling systems |
| 11:55-12:15 | Christopher Zopf, Massachusetts Institute of Technology, Single promoters as regulatory network motifs |
| 12:15-14:30 | Lunch, Dining Hall (service 11:30-13:30) |
| 14:30-18:15 | Session IV, Great Hall, Chair: Gnana Gnanakaran, Los Alamos National Laboratory |
| 14:30-15:00 | Alan Perelson, Los Alamos National Laboratory, Multiscale Modeling of Hepatitis C Virus Infection |
| 15:00-15:20 | Cheemeng Tan , Carnegie Mellon University, The inoculum effect and band-pass bacterial response to periodic antibiotic treatment |
| 15:20-15:40 | Ni Ji, Massachusetts Institute of Technology, _Genetic redundancy in the Wnt pathway promotes robust control of neuronal migration through interlocked feedback loops |
| 15:40-16:00 | Karina Mazzitello, Universidad Nacional de Mar del Plata, Modeling Morphology Dynamics of Retinal Pigment Epithelium |
| 16:00-16:30 | Coffee Break |
| 16:30-16:45 | Poster 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 | |
| 16:45-17:15 | Michael Laub, Massachusetts Institute of Technology and Howard Hughes Medical Institute, Specificity and Evolution of Bacterial Signaling Pathways |
| 17:15-17:35 | Howard Salis, Pennsylvania State University, Automated Design of Synthetic Bacterial Small RNAs |
| 17:35-17:55 | Mark Maienschein-Cline, University of Chicago, Identification of transcription factor targets by analysis of high-throughput data |
| 17:55-18:15 | Veronika Zarnitsyna, Georgia Institute of Technology, Kinetics of molecular interactions across the T cell – APC junction |
| 18:15-18:30 | Break |
| 18:30-20:00 | Dinner (service), Koi Pond |
| 19:00-20:00 | Session V, Koi Pond, Chair: Michael Wall, Los Alamos National Laboratory |
| 19:00-19:05 | Introduction on the Social Aspects of Science |
| 19:05-20:00 | Guitar Session: Love and Fear in the Lab, Uri Alon, Weizmann Institute |
| 20:00-23:00 | Poster Session II ( [_blank q-Bio-Poster-Set-2b] ) |
| Saturday | August 13, 2011 |
| 7:30-9:10 | Breakfast, Dining Hall (service 7:30-9:30) |
| 9:10-12:30 | Session VI, Great Hall, Chair: Brian Munsky, Los Alamos National Laboratory |
| 9:10-9:40 | Nicole King, University of California, Berkeley, The origin of animal multicellularity |
| 9:40-10:00 | Evgeni 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 |
| 10:00-10:20 | Rebecca McLennan, Stowers Institute for Medical Research, Elucidating multiscale mechanisms of neural crest migration |
| 10:20-10:50 | Wallace Marshall, University of California, San Francisco, Biological Noise at the level of Cellular Structure |
| 10:50-11:20 | Coffee Break |
| 11:20-11:50 | Stas Shvartsman, Princeton University, Multiscale studies of embryonic development: experiments and theory |
| 11:50-12:10 | Stephen Helms, University of Texas Southwestern Medical Center, A Tandem PDZ Domain Redox Switch in InaD |
| 12:10-12:30 | Domitilla Del Vecchio, Massachusetts Institute of Technology, The Impact of Retroactivity on the Signal Processing of Transduction Networks |
| 12:30-14:30 | Lunch, Dining Hall (service 11:30-13:30) |
| 14:30-18:10 | Session VII, Great Hall, Chair: Ilya Nemenman, Emory University |
| 14:30-15:00 | Alexander Hoffmann, University of California, San Diego, Parsimonious Gene Regulatory Network modeling reveals mRNA half-life control of the pathogen-responsive transcriptome |
| 15:00-15:20 | Bernie Daigle, Jr., University of California, Santa Barbara, Accelerated Maximum Likelihood Estimation for Stochastic Biochemical Systems |
| 15:20-15:40 | Alistair Boettiger, University of California, Berkeley, No Compromise: Single molecule imaging reveal mechanisms for speed and precision in developmental gene expression |
| 15:40-16:10 | Vittorio Cristini, University of New Mexico, Tumor Modeling |
| 16:10-16:40 | Coffee Break |
| 16:40-17:10 | Michael Deem, Rice University, Heterogeneous Diversity of Spacers within CRISPR |
| 17:10-17:30 | Qiong Yang, Stanford University, Switch-like negative feedback promotes clock-like mitotic oscillation |
| 17:30-17:50 | Alexandra Jilkine, University of Arizona, A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules |
| 17:50-18:10 | Wan-Chen Lin, University of California, Berkeley, Spatial organization in cell membranes |
| 18:10-18:30 | Break |
| 18:30-20:30 | Closing Banquet, Dining Hall |
| 18:30-18:35 | Farewell, Michael Wall, Los Alamos National Laboratory |
| 18:35-19:30 | Dinner |
| 19:30-19:35 | Banquet Speaker Introduction, William Hlavacek, Los Alamos National Laboratory and Translational Genomics Research Institute |
| 19:35-20:30 | Closing Banquet Talk, Peter Sorger, Harvard Medical School, Measuring and Modeling Cell Decision Processes |
| Sunday | August 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
- Second Workshop on Rule-based Modeling of Biochemical Systems (August 14, 2011) - Organizers: Michael L. Blinov, Vincent Danos, James R. Faeder, S. Gnanakaran and William S. Hlavacek
