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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
IMA Live Streaming and Webcasting Photo Gallery Maps
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 (The University of Texas) EE/CS 3-180
10:10a-10:50a Noise and dynamics of the flagellar length control system Wallace Marshall (University of California) 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 (The University of Texas) 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) 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 Duane Nykamp (University of Minnesota) 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

Name Department Affiliation
Steven J. Altschuler Department of Pharmacology UT Southwestern Medical Center
Sigurd B. Angenent Department of Mathematics University of Wisconsin
Ping Ao Department of Mechanical Engineering University of Washington
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
Ahmet Ay Department of Mathematics Michigan State University
Daniel J. Bates Institute for Mathematics and its Applications University of Minnesota
John Baxter Institute for Mathematics and its Applications University of Minnesota
Banu Baydil Department of Mathematical Sciences Rensselaer Polytechnic Institute
Philip Benfey Department of Biology Duke University
Yermal Sujeet Bhat Institute for Mathematics and its Applications University of Minnesota
Khalid Boushaba Department of Mathematics Iowa State University
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Hannah Callender Institute for Mathematics and its Applications University of Minnesota
Enrico Capobianco Bioinformatics Lab Center for Advanced Studies, Research and Development in Sardinia
Hegang Chen School of Medicine, Division of Biostatistics and Bioinformatics University of Maryland at Baltimore
Jie Chen Department of Mathematics and Statistics University of Missouri
John Chen Department of Mathematics and Statistics Bowling Green State University
Ludovica Cecilia Cotta-Ramusino Institute for Mathematics and its Applications University of Minnesota
Gaudenz Danuser Department of Cell Biology Scripps Research Institute
Peter N. Devreotes School of Medicine Johns Hopkins University
Glenn Edwards Department of Physics Duke University
Walid Fakhouri Department of Biochemistry and Molecular Biology Michigan State University
Daniel S. Fisher Applied Physics Department Stanford University
Azamed Yehuala Gezahagne Department of Mathematics East Tennessee State University
Byron Goldstein Department of Theoretical Biology and Biophysics Los Alamos National Laboratory
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
H. Christian Gromoll Department of Mathematics University of Virginia School of Medicine
Esfandiar Haghverdi School of Informatics Indiana University
Jeff Hasty Bioengineering Department University of California, San Diego
Milena Hering Institute for Mathematics and its Applications University of Minnesota
Franziska Babette Hinkelmann Department of Mathematics Virginia Polytechnic Institute and State University
Peter Hinow Institute for Mathematics and its Applications University of Minnesota
Alexander Hoffmann Department of Chemistry and Bio-Chemistry University of California, San Diego
Valerie Marie Hower Department of Cancer Biology Wake Forest Medical School
Wilhelm Huisinga Hamilton Institute National University of Ireland, Maynooth
David Isaacson Department of Mathematical Sciences Rensselaer Polytechnic Institute
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Kevin Janes Department of Cell Biology Harvard Medical School
Imre M. Jánosi Department of Physics of Complex Systems Eötvös Loránd University (ELTE)
Abdul Salam Jarrah Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Tiefeng Jiang Department of Statistics University of Minnesota
Li Jun Microbiology University of Minnesota
Jeff Kearns Department of Chemistry & Biochemistry University of California, San Diego
Debra Knisley Department of Mathematics East Tennessee State University
Markus Kollmann Institute of Theoretical Biology Humboldt-Universität
Peter R. Kramer Department of Mathematical Sciences Rensselaer Polytechnic Institute
Chin-Jen Ku Department of Pharmacology UT Southwestern Medical Center
David Largaespada Department of Genetics, Cell Biology, and Development University of Minnesota
Juan Latorre Department of Mathematical Sciences Rensselaer Polytechnic Institute
Reinhard Laubenbacher Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Christopher J. Lee Department of Chemistry and Bio-Chemistry University of California
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
Paul Loriaux   University of California, San Diego
Roger Y. Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
Yi Mao Department of Mathematics Michigan State University
M. David Marks Department of Plant Biology University of Minnesota
Elisabetta Marras Bioinformatics Department CRS4 Bioinformatics Laboratory,
Wallace Marshall Department of Biochemistry and Molecular Biophysics University of California
Ana Margarida Martins Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
George Michailidis Department of Statistics University of Michigan
Ezra Miller School of Mathematics University of Minnesota
Joachim Mueller Department of Physics University of Minnesota
Arcady Mushegian   Stowers Institute
Timothy Newman Department of Physics Arizona State University
Amir Niknejad Department of Mathematics East Tennessee State University
Duane Nykamp School of Mathematics University of Minnesota
David Odde Department of Biomedical Engineering University of Minnesota
Hans G. Othmer Department of Mathematics University of Minnesota
Antonis Papachristodoulou Department of Engineering Science University of Oxford
Bobby Philip Computer and Computational Sciences Division Los Alamos National Laboratory
Mary Porter Department of Genetics, Cell Biology, and Development University of Minnesota
Olivier Pourquié   Stowers Institute
Ashok Prasad Chemical Engineering Department Massachusetts Institute of Technology
Vito Quaranta Cancer Biology Vanderbilt University
Mahalingam Ramkumar Computer Science Mississippi State University
Rama Ranganathan UT Southwestern Medical Center at Dallas The University of Texas
Eric J. Rawdon Department of Mathematics University of St. Thomas
Brandon Razooky Department of Biochemistry University of California, San Diego
Timothy Charles Reluga Department of Mathematics Pennsylvania State University
Dipen Sanguvdekes Chemical Engineering University of Minnesota
Deena Schmidt Institute for Mathematics and its Applications University of Minnesota
Gaukhar Shaikhova Department of Mathematics and Information Technology The L.N.Gumilyov Eurasian National University
Chehrzad Shakiban Institute of Mathematics and its Application University of Minnesota
Danying Shao Center for Theoretical Biological Physics University of California, San Diego
Andrey Shilnikov Department of Mathematics and Statistics Georgia State University
Ali Shojaie Department of Statistics University of Michigan
Dinesh Kumar Singh Green Centre for Systems Biology UT Southwestern Medical Center
Kim Sneppen Center for Models of Life University of Copenhagen
Eduardo D. Sontag Department of Mathematics Rutgers University
Andrew Stein Institute for Mathematics and its Applications University of Minnesota
Victoria Anne Stokes School of Biology University of St. Andrews
Gürol Süel The University of Texas Southwestern Medical Center at Dallas The University of Texas
De Witt L. Sumners Department of Mathematics Florida State University
Vladimir Sverak School of Mathematics University of Minnesota
Peter Swain Department of Physiology McGill University
Lev S. Tsimring Institute for Nonlinear Science University of California, San Diego
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
Jin Wang Department of Chemistry, Physics and Applied Mathematics SUNY
Yanqin Wang Department of Pharmacology UT Southwestern Medical Center
Yu-Ping Wang Department of Electrical Engineering and Computer Science University of Missouri
Zhian Wang Institute for Mathematics and its Applications University of Minnesota
Hans Weinberger School of Mathematics University of Minnesota
Leor Weinberger Department of Chemistry and Biochemistry University of California, San Diego
H. Steven Wiley Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory
Ruth J. Williams Department of Mathematics University of California, San Diego
Lani Wu Department of Pharmacology UT Southwestern Medical Center
Zhijun Wu Department of Mathematics Iowa State University
Sichun Yang Department of Biochemistry and Molecular Biology University of Chicago
Yingfei Yi School of Mathematics Georgia Institute of Technology
Changhe Yuan Department of Computer Science and Engineering Mississippi State University
Gao Zhang Department of Bioengineering University of Pennsylvania
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota
Linghai Zhang Department of Mathematics Lehigh University