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{{q-bio conference}} You may also want to view the program of the associated [[First q-bio Summer School: Program | Summer School]]. ==News== A report on the First q-bio Conference was published in [http://www.nature.com/msb/journal/v3/n1/full/msb4100193.html Molecular Systems Biology] ([http://cnls.lanl.gov/q-bio/wiki/images/2/26/Edwards-MSB-2007.pdf pdf]). ==Participants== *[[First q-bio Conference: Organizers | Organizers]] *[[First q-bio Conference: Speakers Presenting Invited Talks | Speakers Presenting Invited Talks]] *[[First q-bio Conference: Speakers Presenting Contributed Talks | Speakers Presenting Contributed Talks]] *[[First q-bio Conference: Speakers Presenting Poster Spotlight Talks | Speakers Presenting Poster Spotlight Talks]] *[[First q-bio Conference: Poster Presentations |First q-bio Conference: Poster Presentations ]] *[[First q-bio Conference: General Participants |General Participants ]] ==Carpools== *[[Carpools from ABQ to St. John's on 08/08/07]] *[[Carpools from ABQ to St. John's on 08/09/07]] *[[Carpools from St. John's to ABQ on 08/11/07]] *[[Carpools from St. John's to ABQ on 08/12/08]] *[[Other carpools]] ==Additional Information== *[[First q-bio Conference: Participants survey| Participants Survey]] *[[First q-bio Conference: Photos| Photos from the Conference]] *[[First q-bio Conference: Poster information| Poster Information]] *[[What to do in the vicinity of Los Alamos | What to do in the vicinity of Santa Fe]] *[http://t8web.lanl.gov/people/salman/sf07/eating.html Eating out] *[[First q-bio Conference: Internet Access| Internet Access]] *[[St John's College campus information]] (conference venue) ==Conference Program== ===Wednesday, Aug 8, 2007=== ;<nowiki>14:00-16:15 Tutorials and Software Demonstrations</nowiki> :14:00-15:00 - [[Tutorial: Complex Systems Biology: In search of Universal Statistical Dynamics in Reproduction, Adaptation, and Phenotypic Evolution]], [http://chaos.c.u-tokyo.ac.jp/ Kunihiko Kaneko] (University of Tokyo) :15:15-16:15 - [[Tutorial: Rule-based modeling using BioNetGen and the Virtual Cell]], [http://genetics.uchc.edu/faculty/blinov.htm Michael Blinov] (University of Connecticut Health Center) ;<nowiki>17:00-17:45 Reception</nowiki>: ;<nowiki>17:45-19:45 Opening Banquet (Great Hall)</nowiki> :17:45-17:50 ''Welcome'', [http://cnls.lanl.gov/External/people/Robert_Ecke.php Robert Ecke] (Director, CNLS, Los Alamos National Laboratory) :17:50-18:00 ''Welcome'', David H. Sharp (Chief Scientific Officer, Los Alamos National Laboratory) :18:00-19:00 Dinner :19:00-19:45 [[Searching for principles]], [http://www.princeton.edu/~wbialek/wbialek.html William Bialek] (Princeton University) ===Thursday, Aug 9, 2007=== ;<nowiki>07:30-08:30 Breakfast</nowiki> :Dining Hall is open 7:30-9:30 ;<nowiki>08:30-12:15</nowiki> Session I - James R. Faeder (chair) :08:30-09:00 [[Physiology and genetic regulation of cellular signal transmission]], [http://www.molsci.org/~brent/ Roger Brent] (Molecular Sciences Institute) :09:00-09:20 Contributed Talk: [[Study of Signal Processing in Quorum Sensing at Single-Cell Level]], Tao Long (Princeton University) :09:20-09:50 [[The Virtual Cell project]], [http://www.ccam.uchc.edu/people/loew/loew.html Leslie M. Loew] (University of Connecticut Health Center) :09:50-10:20 [[Regulatory genome information processing during early development in the sea urchin]], [http://www.its.caltech.edu/~mirsky/labm/smadar.htm Smadar Ben-Tabou De-Leon] (California Institute of Technology) :10:20-10:45 Coffee Break :10:45-10:55 Poster Spotlights ::[[Modeling the Oscillatory Response of the NF-κB Signaling Pathway]], Diane Longo (UC San Diego) ::[[How Cells Decide Between Apoptosis and Survival in Response to DNA Damage]], Gerry Ostheimer (MIT) ::[[Switching gene-regulatory loops in Th1 differentiation]], Edda Schulz (Humboldt) :10:55-11:25 [[Optimization of the cellular response and searching strategy in bacterial chemotaxis]], [http://www.biology.yale.edu/facultystaff/emonet.html Thierry Emonet] (Yale) :11:25-11:45 Contributed Talk: [[Live Cell Imaging Methods to Quantify Signaling Molecule Dynamics]], [http://hsc.unm.edu/research/facultyprofiles/index.cfm?m=main.faculty&unique_id=4D61B996F85D4AB38ED5B243BCACC7A92DCE2B0C Diane Lidke] (UNM) :11:45-12:15 [[Systems biology of the Drosophila blastoderm: what can we learn?]], [http://flyex.ams.sunysb.edu/ John Reinitz] (Stony Brook University) ;<nowiki>12:15-14:00</nowiki> Lunch :Dining Hall is open 11:30-1:30 ;<nowiki>14:00-17:45</nowiki> Session II - William S. Hlavacek (chair) :14:00-14:30 [[Investigating a temporal code of inflammatory signaling]], [http://signalingsystems.ucsd.edu/ Alexander Hoffmann] (UC San Diego) :14:30-14:50 Contributed Talk: [[Metabolic gene regulation in a dynamically changing environment]], [http://biodynamics.ucsd.edu/profiles/matt.htm Matthew Bennett] (UC San Diego) :14:50-15:20 [[Specificity in Bacterial Two-Component Signaling]], [http://www.physics.upenn.edu/facultyinfo/goulian.html Mark Goulian] (University of Pennsylvania) :15:20-15:50 [[Reconstruction of the genome-scale transcriptional regulatory network in E. coli]], [http://gcrg.ucsd.edu/personnel/palsson.htm Bernhard Ø. Palsson] (University of California, San Diego) :15:50-16:15 Coffee Break :16:15-16:25 Poster Spotlights ::<strike>[[Activating Ras Mutations in vitro and in Cancer]], Edward Stites (U of Virginia)</strike> Fangping Mu (LANL) ::[[Probabilistic Modeling & Analysis of Switch-Like Signal Transduction Systems]], Marc Birtwistle (University of Delaware) ::[[Quantitative assessment of endothelial cell response to spatial gradients of VEGF]], David Noren (Johns Hopkins U) :16:25-16:55 [[Signaling through cAMP and cAMP-dependent Protein Kinase]], [http://tayloradmin-g4.ucsd.edu/ Susan Taylor] (UC San Diego) :16:55-17:15 Contributed Talk: [[Engineering the Salmonella SPI-1 System for Heterologous Protein Production]], Danielle Tullman-Ercek (UC San Francisco) :17:15-17:45 [[Exploring the Design Space of MAP Kinase Cascades]], [http://www.ucsf.edu/limlab/people/noah.html Noah Helman] (UC San Francisco) ;<nowiki>17:45-20:15</nowiki> Dinner :charter bus service to downtown locations ;<nowiki>20:15-22:45 Poster Session 1</nowiki> ===Friday, Aug 10=== ;<nowiki>07:30-08:30</nowiki> Breakfast :Dining Hall is open 7:30-9:30 ;<nowiki>08:30-12:15</nowiki> Session III - Michael E. Wall (chair) :08:30-09:00 [[Engineered Gene Circuits]], [http://biodynamics.ucsd.edu/profiles2/jeff.htm Jeff Hasty] (University of California, San Diego) :09:00-09:20 Contributed Talk: [[Correlation and Causality in Genetic Networks]], [http://www.its.caltech.edu/~mjdunlop/ Mary Dunlop] (Caltech) :09:20-09:50 [[Systems Behavior in Phage λ and Evolution of Complex Regulatory Circuitry]], [http://www.biochem.arizona.edu/dept/ppl/Profiles/little.htm John W. Little] (University of Arizona) :09:50-10:20 [[Quantifying Biological Performance in System Design Space]], [http://www.bme.ucdavis.edu/profile/masavageau/ Michael A. Savageau] (University of California, Davis) :10:20-10:45 Coffee Break :10:45-10:55 Poster Spotlights ::[[Open Complex Formation by Bacterial RNA Polymerase - a Quantitative Model]], Marko Djordjevic (Ohio State) ::[[Stochastic model for IL-4 expression dynamics]], Luca Mariani (Humboldt U) ::[[Physical theory of nucleo-cytoplasmic transport]], Anton Zilman (LANL) :10:55-11:25 [[Pre-Existing Variation Controls the Lysis-Lysogeny Decision in Phage Lambda Infection]], [http://openwetware.org/wiki/Endy_Lab Drew Endy] (Massachusetts Institute of Technology) :11:25-11:45 Contributed Talk: [[Variability dynamics of protein levels in human cells]], Alex Sigal (Caltech) :11:45-12:15 [[Casting a Net for Kinases - Probabilistic Modeling of Cellular Signaling Systems]], [http://synthbio.mshri.on.ca/linding.eu/Welcome.html Rune Linding] (Samuel Lunenfeld Research Institute) ;<nowiki>12:15-14:00</nowiki> Lunch :Dining Hall is open 11:30-1:30 ;<nowiki>14:00-17:45</nowiki> Session IV - Yi Jiang (chair) :14:00-14:30 [[Mapping and modeling receptor topography during signal transduction]], [http://cellpath.health.unm.edu/faculty/Bridget/bridget.html Bridget S. Wilson] (University of New Mexico) :14:30-14:50 Contributed Talk: [[Finite State Projection Solutions to the CME Arising in Gene Regulatory Networks]], [http://www.uweb.ucsb.edu/~brian_munsky/ Brian Munsky] (UCSB) :14:50-15:20 [[Dynamics of signal transduction and gene expression in single cells]], [http://web.mit.edu/biophysics/ Alexander van Oudenaarden] (Massachusetts Institute of Technology) :15:20-15:50 [[How to move through a very dense crowd]], [http://cmgm.stanford.edu/devbio/kaiserlab/ Dale Kaiser] (Stanford University) :15:50-16:15 Coffee Break :16:15-16:25 Poster Spotlights ::[[Fly Magnetism: Planar cell polarity in the wing]], Yoram Burak (UC Santa Barbara) ::[[Coarse-graining biochemical reactions]], Nikolai Sinitsyn (LANL) ::[[Quantitative Analysis of HER2 Overexpression Effect on EGF Receptor Signaling]], Yi Zhang (PNNL) :16:25-16:55 [[Optimal path to epigenetic switching]], [http://www.physics.rutgers.edu/~anirvans/ Anirvan Sengupta] (Rutgers) :16:55-17:15 Contributed Talk: [[Sensitivity, feedback and fluctuations in bacterial chemotaxis]], [http://www.rowland.harvard.edu/labs/bacteria/people_tshimizu.html Thomas Shimizu] (Harvard University) :17:15-17:45 [[Trade-offs and limits in feedback-driven noise suppression]], [http://paulsson.med.harvard.edu/Paulsson_Lab_files/page0004.htm Johan Paulsson] (Harvard Medical School) ;<nowiki>17:45-20:15</nowiki> Dinner :Charter bus service to downtown locations ;<nowiki>20:15-22:45</nowiki> Poster Session 2 ===Saturday, Aug 11, 2007=== ;<nowiki>07:30-08:30</nowiki> Breakfast :Dining Hall is open 7:30-9:30 ;<nowiki>08:30-12:15</nowiki> Session V - Ilya Nemenman (chair) :08:30-09:00 [[Information processing by gradient sensing system: convergence of methods, divergence of means]], [https://jshare.johnshopkins.edu/alevche1/web/ Andre Levchenko] (Johns Hopkins University) :09:00-09:20 Contributed Talk: [[Form, Function, and Information Processing in Small Stochastic Biological Networks]], [http://www.columbia.edu/~chw2/ Chris Wiggins] (Columbia University) :09:20-09:50 [[Adaptation of genetic regulatory networks and its role in cell evolvability]], [http://www.technion.ac.il/~nbrenner/index_on_hold.htm Naama Brenner] (Technion-Israel Institute of Technology) :09:50-10:20 [[(De)constructing cellular networks]], [http://genomics.lbl.gov/ Adam P. Arkin] (Lawrence Berkeley National Laboratory) :10:20-10:45 Coffee Break :10:45-11:15 [[Stochastic dynamics of macromolecular-assembly networks]], [http://cbio.mskcc.org/~vilar/ Jose M. G. Vilar] (Sloan-Kettering Institute) :11:15-11:45 [[From molecules to behavior: Understanding responses of E. coli to complex temporal signals]], [http://domino.research.ibm.com/comm/research_people.nsf/pages/yuhaitu.index.html Yuhai Tu] (IBM T.J. Watson Research Center) :11:45-12:15 [[Systematic Analysis of Crosstalk in the PDGF Receptor Signal Transduction Network]], [http://www.che.ncsu.edu/faculty_staff/jmh.html Jason M. Haugh] (North Carolina State University) ;<nowiki>12:15-14:00</nowiki> Lunch :Dining Hall is open 11:30-13:30 ;<nowiki>14:00-18:15</nowiki> Session VI - Byron Goldstein (chair) :14:00-14:30 [[Probing Transcription Factor Dynamics at the Single Molecule Level in a Living Cell]], [http://www.people.fas.harvard.edu/~elf/ Johan Elf] (Harvard University) :14:30-15:00 [[How T cells see antigen]], [http://web.mit.edu/cheme/people/faculty/chakraborty.html Arup K. Chakraborty] (Massachusetts Institute of Technology) :15:00-15:20 Contributed Talk: [[Applications of sensitivity analysis for drug discovery and development in the ErbB network]], Birgit Schoeberl (Merrimack Pharmaceuticals) :15:20-15:50 [[Graph Theory Based Hypotheses with Experimental Validation to Identify Novel Functions of Components and Pathways in Mammalian Cells]], [http://www.mssm.edu/labs/iyengar/bios/maayan.shtml Avi Ma'ayan] (Mount Sinai School of Medicine) :15:50-16:15 Coffee Break :16:15-16:45 [[Cell Signaling Dynamics in Time and Space]], [http://www.jefferson.edu/pathology/faculty_profile.cfm?key=bxk110 Boris N. Kholodenko] (Thomas Jefferson University) :16:45-17:15 [[Quantitative phosphoproteomics in cell signaling]], [http://www1.sdu.dk/Nat/bmb/postdocs/blagoev_b.html Blagoy Blagoev] (University of Southern Denmark) :17:15-17:45 [[Autocrine signaling and feedback loops in the EGF receptor system]], [http://www.sysbio.org/resources/staff/wiley.stm H. Steven Wiley] (Pacific Northwest National Laboratory) :17:45-18:15 [[Rule-based modeling of signal-transduction systems]], [http://www.t10.lanl.gov/faeder/ James R. Faeder] (University of Pittsburgh School of Medicine) ;<nowiki>18:15-18:45 Break</nowiki> ;<nowiki>18:45-20:45 Closing Banquet (Dining Hall)</nowiki> :18:45-19:00 ''Farewell'', Organizers :19:00-20:00 Dinner :20:00-20:45 [[Rules of engagement: The architecture of robust, evolvable networks]], [http://www.cds.caltech.edu/~doyle/home.htm John Doyle] (California Institute of Technology) [http://www.cds.caltech.edu/~doyle/2007_06 Slides]

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