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.
(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.
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
|
|
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 |
| 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 | School of Mathematics | University of Minnesota |
| Ahmet Ay | Department of Mathematics | Michigan State University |
| Daniel J. Bates | 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 Biochemistry | University of California, San Diego |
| Valerie 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 | Department of 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 C. 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 Biochemistry | University of California, Los Angeles |
| Anton Leykin | Institute for Mathematics and its Applications | University of Minnesota |
| Paul Loriaux | | University of California, San Diego |
| Roger 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, San Francisco |
| 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 J. 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 | Department of Cancer Biology | Vanderbilt University |
| Mahalingam Ramkumar | Computer Science Department | Mississippi State University |
| Rama Ranganathan | | UT Southwestern Medical Center |
| 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 | Department of 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 M. Stein | Institute for Mathematics and its Applications | University of Minnesota |
| Victoria Anne Stokes | School of Biology | University of St. Andrews |
| Gürol Süel | Department of Pharmacology | UT Southwestern Medical Center |
| 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 | Enviromental 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 |