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IMA Annual Program Year Workshop

Organization of Biological Networks

March 3-7, 2008
Organizers:
Steven J. Altschuler Pharmacology, University of Texas Southwestern Medical Center at Dallas
Alexander Hoffmann Chemistry and Biochemistry, University of California at San Diego
Lani Wu Pharmacology, University of Texas Southwestern Medical Center at Dallas

Schedule Participants Program Application Feedback
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Abstracts and Talk Materials Dining Guide

Scientific Background:

Research towards understanding biological systems is moving from a focus of identifying components parts (cells, molecules, sequences) to the study of how these components function together. Networks attain functional characteristics that the individual components do not possess in isolation. To reveal and further explore such emergent properties of networks, over a variety of biological scales and complexities, mathematical tools play increasingly important roles in furthering our understanding of biological systems.

Goals:

(1) The goal of this workshop is to bring together researchers from the biological and mathematical sciences to address emergent systems properties. This workshop will not focus on tool building for data analysis, but modeling for hypothesis generation.

(2) The goal of each session is to first discuss progress and challenges at a specific biological scale.

(3) The goal for each presenter is to involve the participants from across disciplines in addressing specific questions in their research. Off-line discussion is a major component of this workshop.

Session Descriptions:

The workshop will be organized into five sessions, presented in increasing order of biological scale: The first session will be at the single molecule scale, with emphasis on stochastic effects. The second will be in design principles of small networks, often studied as engineered or "synthetic" networks. The third and fourth sessions will delve into intra- and intercellular networks. Our final session will cover design principles of large networks, including results from interpreting high-throughput and large-scale datasets.

Schedule
Monday | Tuesday | Wednesday | Thursday | Friday | 
  Monday, March 3
8:15a-9:00a Registration and coffee   EE/CS 3-176
9:00a-9:20a Welcome to the IMA and introduction by the organizers Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:20a-10:00a The evolutionary design of proteins Rama Ranganathan (UT Southwestern Medical Center) EE/CS 3-180
10:10a-10:50a Noise and dynamics of the flagellar length control system Wallace Marshall (University of California, San Francisco) EE/CS 3-180
10:50a-11:20a Coffee   EE/CS 3-176
11:20a-12:00p Noisy out of necessity: Probabilistic behavior in cellular differentiation Gürol Süel (UT Southwestern Medical Center) EE/CS 3-180
12:00p-2:00p Lunch    
2:00p-2:40p Transient decision making in a transcriptional circuit of HIV-1 Leor Weinberger (University of California, San Diego) EE/CS 3-180
2:50p-3:30p Quantifying and predicting gene regulation in single cells Peter Swain (McGill University) EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:30p Second chances   EE/CS 3-180
4:30p-4:45p Group Photo    
4:45p-6:30p Reception and Poster Session
Lind Hall 400
Predictive models of Cis-regulatory transcriptional grammar Ahmet Ay (Michigan State University)
Multiscale tour in protein interactomics Enrico Capobianco (Center for Advanced Studies, Research and Development in Sardinia)
Elisabetta Marras (CRS4 Bioinformatics Laboratory, )
Multiscale look in protein interactomics Enrico Capobianco (Center for Advanced Studies, Research and Development in Sardinia)
Elisabetta Marras (CRS4 Bioinformatics Laboratory, )
Using CellDesigner to create the iron metabolic network Valerie Marie Hower (Wake Forest Medical School)
A mathematical model of the TNF signaling network controlling apoptosis via NF-kB and JNK Paul Loriaux (University of California, San Diego)
Gene vectors and distances between them: the neglected aspect of network biology Arcady Mushegian (Stowers Institute)
From systems to synthetic biology: A control theoretic approach Antonis Papachristodoulou (University of Oxford)
Digital negative and analog positive selection thresholds in T cells: A molecular model Ashok Prasad (Massachusetts Institute of Technology)
Analysis of gene sets based on the underlying regulatory network Ali Shojaie (University of Michigan)
Homotopy methods for counting reaction network equilibria Ruth J. Williams (University of California, San Diego)
Joint analysis of gene expression and gene copy number variations using independent component analysis Yu-Ping Wang (University of Missouri)
Nonlinear traveling waves in synaptically coupled neuronal networks Linghai Zhang (Lehigh University)
Speed analysis of traveling wave solutions of some nonlocal evolutionary equations Linghai Zhang (Lehigh University)
  Tuesday, March 4
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:40a Qualitative/quantitative analysis of biomolecular network dynamics Eduardo D. Sontag (Rutgers University) EE/CS 3-180
9:50a-10:30a The spontaneous emergence of cell polarity Sigurd B. Angenent (University of Wisconsin) EE/CS 3-180
10:30a-11:00a Coffee   EE/CS 3-176
11:00a-11:40a Circadian clocks and switches in cynanobacteria Daniel S. Fisher (Stanford University) EE/CS 3-180
11:40a-2:00p Lunch    
2:00p-2:40p Mapping evolutionary pathways of HIV-1 drug resistance using conditional selection pressure Christopher J. Lee (University of California, Los Angeles) EE/CS 3-180
2:50p-3:30p Robustness of signal processing in bacterial chemotaxis Markus Kollmann (Humboldt-Universität) EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:15p A "bottom-up" approach to deciphering and predicting cis-regulatory transcriptional grammar in Drosophila Walid Fakhouri (Michigan State University) EE/CS 3-180
4:20p-4:50p Second chances   EE/CS 3-180
5:00p-6:30p Math matters public lecture reception   Lind Hall 400
7:00p-8:15p Math matters public lecture: The best of all possible worlds: The idea of optimization Ivar Ekeland (University of British Columbia) Willey Hall 125
  Wednesday, March 5
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:40a Engineered gene circuits Jeff Hasty (University of California, San Diego) EE/CS 3-180
9:50a-10:30a Adaptation-driven models of cancer invasion: Experimental parameterization and validation Vito Quaranta (Vanderbilt University) EE/CS 3-180
10:30a-11:00a Coffee   EE/CS 3-176
11:00a-11:40a Identifying transcriptional dichotomies by stochastic sampling Kevin Janes (Harvard Medical School) EE/CS 3-180
11:40a-2:00p Lunch    
2:00p-2:40p Bayesian network algorithms for revealing structure of complex biological networks Victoria Anne Stokes (University of St. Andrews) EE/CS 3-180
2:50p-3:30p Estimating neuronal network connectivity   EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:50p Second chances   EE/CS 3-180
  Thursday, March 6
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:40a Modeling histone mediated epigenetics as a positive feedback process Kim Sneppen (University of Copenhagen) EE/CS 3-180
9:50a-10:30a Signaling networks in chemotaxis and cytokinesis Peter N. Devreotes (Johns Hopkins University) EE/CS 3-180
10:30a-11:00a Coffee   EE/CS 3-176
11:00a-11:40a Drosophila morphogenesis: Tissue dynamics and emergent properties during dorsal closure Glenn Edwards (Duke University) EE/CS 3-180
11:40a-2:00p Lunch    
2:00p-2:40p Inference of morphogenic pathways from live cell images Gaudenz Danuser (Scripps Research Institute) EE/CS 3-180
2:50p-3:30p Modularity, feedback and recursion in the EGF receptor system H. Steven Wiley (Pacific Northwest National Laboratory) EE/CS 3-180
3:30p-4:00p Coffee   EE/CS 3-176
4:00p-4:50p Second chances   EE/CS 3-180
6:30p-8:30p Workshop Dinner   Kikugawa at Riverplace
43 Main Street SE Minneapolis MN 55414
612-378-3006 
  Friday, March 7
8:30a-9:00a Coffee   EE/CS 3-176
9:00a-9:40a The vertebrate segmentation clock: converting time into embryonic pattern Olivier Pourquié (Stowers Institute) EE/CS 3-180
9:50a-10:30a Root networks: inside out Philip Benfey (Duke University) EE/CS 3-180
10:30a-11:00a Coffee   EE/CS 3-176
11:00a-11:30a Second chances and closing remarks   EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

NameDepartmentAffiliation
Steven J. AltschulerDepartment of Pharmacology UT Southwestern Medical Center
Sigurd B. AngenentDepartment of Mathematics University of Wisconsin
Ping AoDepartment of Mechanical Engineering University of Washington
Douglas N. ArnoldSchool of Mathematics University of Minnesota
Ahmet AyDepartment of Mathematics Michigan State University
Daniel J. BatesInstitute for Mathematics and its Applications University of Minnesota
Banu BaydilDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Philip BenfeyDepartment of Biology Duke University
Yermal Sujeet BhatInstitute for Mathematics and its Applications University of Minnesota
Khalid BoushabaDepartment of Mathematics Iowa State University
Maria-Carme T. CaldererSchool of Mathematics University of Minnesota
Hannah CallenderInstitute for Mathematics and its Applications University of Minnesota
Enrico CapobiancoBioinformatics Lab Center for Advanced Studies, Research and Development in Sardinia
Hegang ChenSchool of Medicine, Division of Biostatistics and Bioinformatics University of Maryland at Baltimore
Jie ChenDepartment of Mathematics and Statistics University of Missouri
John ChenDepartment of Mathematics and Statistics Bowling Green State University
Ludovica Cecilia Cotta-RamusinoInstitute for Mathematics and its Applications University of Minnesota
Gaudenz DanuserDepartment of Cell Biology Scripps Research Institute
Peter N. DevreotesSchool of Medicine Johns Hopkins University
Glenn EdwardsDepartment of Physics Duke University
Walid FakhouriDepartment of Biochemistry and Molecular Biology Michigan State University
Daniel S. FisherApplied Physics Department Stanford University
Azamed Yehuala GezahagneDepartment of Mathematics East Tennessee State University
Byron GoldsteinDepartment of Theoretical Biology and Biophysics Los Alamos National Laboratory
Jason E. GowerInstitute for Mathematics and its Applications University of Minnesota
H. Christian GromollDepartment of Mathematics University of Virginia School of Medicine
Esfandiar HaghverdiSchool of Informatics Indiana University
Jeff HastyBioengineering Department University of California, San Diego
Milena HeringInstitute for Mathematics and its Applications University of Minnesota
Franziska Babette HinkelmannDepartment of Mathematics Virginia Polytechnic Institute and State University
Peter HinowInstitute for Mathematics and its Applications University of Minnesota
Alexander HoffmannDepartment of Chemistry and Biochemistry University of California, San Diego
Valerie HowerDepartment of Cancer Biology Wake Forest Medical School
Wilhelm HuisingaHamilton Institute National University of Ireland, Maynooth
David IsaacsonDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Richard D. JamesDepartment of Aerospace Engineering and Mechanics University of Minnesota
Kevin JanesDepartment of Cell Biology Harvard Medical School
Imre M. JánosiDepartment of Physics of Complex Systems Eötvös Loránd University (ELTE)
Abdul Salam JarrahVirginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Tiefeng JiangDepartment of Statistics University of Minnesota
Li JunDepartment of Microbiology University of Minnesota
Jeff KearnsDepartment of Chemistry & Biochemistry University of California, San Diego
Debra KnisleyDepartment of Mathematics East Tennessee State University
Markus KollmannInstitute of Theoretical Biology Humboldt-Universität
Peter R. KramerDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Chin-Jen KuDepartment of Pharmacology UT Southwestern Medical Center
David LargaespadaDepartment of Genetics, Cell Biology, and Development University of Minnesota
Juan C. LatorreDepartment of Mathematical Sciences Rensselaer Polytechnic Institute
Reinhard LaubenbacherVirginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Christopher J. LeeDepartment of Chemistry and Biochemistry University of California, Los Angeles
Anton LeykinInstitute for Mathematics and its Applications University of Minnesota
Paul Loriaux University of California, San Diego
Roger LuiDepartment of Mathematical Sciences Worcester Polytechnic Institute
Laura LuratiInstitute for Mathematics and its Applications University of Minnesota
Yi MaoDepartment of Mathematics Michigan State University
M. David MarksDepartment of Plant Biology University of Minnesota
Elisabetta MarrasBioinformatics Department CRS4 Bioinformatics Laboratory,
Wallace MarshallDepartment of Biochemistry and Molecular Biophysics University of California, San Francisco
Ana Margarida MartinsVirginia Bioinformatics Institute Virginia Polytechnic Institute and State University
George MichailidisDepartment of Statistics University of Michigan
Ezra MillerSchool of Mathematics University of Minnesota
Joachim MuellerDepartment of Physics University of Minnesota
Arcady Mushegian Stowers Institute
Timothy NewmanDepartment of Physics Arizona State University
Amir NiknejadDepartment of Mathematics East Tennessee State University
Duane NykampSchool of Mathematics University of Minnesota
David J. OddeDepartment of Biomedical Engineering University of Minnesota
Hans G. OthmerDepartment of Mathematics University of Minnesota
Antonis PapachristodoulouDepartment of Engineering Science University of Oxford
Bobby PhilipComputer and Computational Sciences Division Los Alamos National Laboratory
Mary PorterDepartment of Genetics, Cell Biology, and Development University of Minnesota
Olivier Pourquié Stowers Institute
Ashok PrasadChemical Engineering Department Massachusetts Institute of Technology
Vito QuarantaDepartment of Cancer Biology Vanderbilt University
Mahalingam RamkumarComputer Science Department Mississippi State University
Rama Ranganathan UT Southwestern Medical Center
Eric J. RawdonDepartment of Mathematics University of St. Thomas
Brandon RazookyDepartment of Biochemistry University of California, San Diego
Timothy Charles RelugaDepartment of Mathematics Pennsylvania State University
Dipen SanguvdekesDepartment of Chemical Engineering University of Minnesota
Deena SchmidtInstitute for Mathematics and its Applications University of Minnesota
Gaukhar ShaikhovaDepartment of Mathematics and Information Technology  The L.N.Gumilyov Eurasian National University
Chehrzad ShakibanInstitute of Mathematics and its Application University of Minnesota
Danying ShaoCenter for Theoretical Biological Physics University of California, San Diego
Andrey ShilnikovDepartment of Mathematics and Statistics Georgia State University
Ali ShojaieDepartment of Statistics University of Michigan
Dinesh Kumar SinghGreen Centre for Systems Biology UT Southwestern Medical Center
Kim SneppenCenter for Models of Life University of Copenhagen
Eduardo D. SontagDepartment of Mathematics Rutgers University
Andrew M. SteinInstitute for Mathematics and its Applications University of Minnesota
Victoria Anne StokesSchool of Biology University of St. Andrews
Gürol SüelDepartment of Pharmacology UT Southwestern Medical Center
De Witt L. SumnersDepartment of Mathematics Florida State University
Vladimir SverakSchool of Mathematics University of Minnesota
Peter SwainDepartment of Physiology McGill University
Lev S. TsimringInstitute for Nonlinear Science University of California, San Diego
Erkan TüzelInstitute for Mathematics and its Applications University of Minnesota
Jin WangDepartment of Chemistry, Physics and Applied Mathematics SUNY
Yanqin WangDepartment of Pharmacology UT Southwestern Medical Center
Yu-Ping WangDepartment of Electrical Engineering and Computer Science University of Missouri
Zhian WangInstitute for Mathematics and its Applications University of Minnesota
Hans WeinbergerSchool of Mathematics University of Minnesota
Leor WeinbergerDepartment of Chemistry and Biochemistry University of California, San Diego
H. Steven WileyEnviromental Molecular Sciences Laboratory Pacific Northwest National Laboratory
Ruth J. WilliamsDepartment of Mathematics University of California, San Diego
Lani WuDepartment of Pharmacology UT Southwestern Medical Center
Zhijun WuDepartment of Mathematics Iowa State University
Sichun YangDepartment of Biochemistry and Molecular Biology  University of Chicago
Yingfei YiSchool of Mathematics Georgia Institute of Technology
Changhe YuanDepartment of Computer Science and Engineering Mississippi State University
Gao ZhangDepartment of Bioengineering University of Pennsylvania
Hongchao ZhangInstitute for Mathematics and its Applications University of Minnesota
Linghai ZhangDepartment of Mathematics Lehigh University