Workshop IV: Systems Biology and Molecular Modeling - IPAM

Workshop IV: Systems Biology and Molecular Modeling

Part of the Long Program Cells and Materials: At the Interface between Mathematics, Biology and Engineering
May 22 - 26, 2006

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, May 22, 2006

Morning Session

08:00-08:45
Check-In/Light Breakfast (Hosted by IPAM)
08:45-09:00
Welcome and Opening Remarks
09:00-10:00
David Stocum (Indiana University - Purdue University)
Self-Organization of the Amphibian Limb Regeneration Blastema: Cellular and Molecular Mechanisms.
10:00-10:30
Break
10:30-11:30
Armin Kaiser (Stanford University)
Bacterial Cooperativity
11:30-14:00
Lunch (on your own)

Afternoon Session

14:00-15:00
Hans Meinhardt (Max-Planck-Institut für Entwicklungsbiologie (Developmental Biology))
Models of biological pattern formation: from elementary steps to the patterning of the main body axes
15:00-15:30
Break
15:30-16:30
Jim McGrath (University of Rochester)
From molecules to monolayers: solving sheet migration with models at every length scale
16:30-17:30
Christoph Adami (Keck Graduate Institute)
Digital Genetics: Unraveling the Genetic Basis of Evolution
17:30-19:00
Wine/Cheese Reception (Hosted by IPAM)

Tuesday, May 23, 2006

Morning Session

08:00-09:00
Continental Breakfast
09:00-10:00
Christopher Rao (University of Illinois at Urbana-Champaign)
Modeling the developmental program for the flagellum and type III secretion apparatus in Salmonella typhimurium
10:00-10:30
Break
10:30-11:30
Michael Samoilov (Howard Hughes Medical Institute)
Quantitative Analysis of Genetic Regulation at Different Scales
11:30-14:00
Lunch (on your own)

Afternoon Session

14:00-15:00
Joel Bader (Johns Hopkins University)
Ab initio predictions of transcription factor binding
15:00-15:30
Break
15:30-16:30
Denise Wolf (Lawrence Berkeley Laboratory)
Diversity in times of adversity: probabilistic strategies in microbial survival games
16:30-17:30
Arthur Lander (University of California, Irvine)
Exploring the performance objectives of morphogen gradient systems

Wednesday, May 24, 2006

Morning Session

08:00-09:00
Continental Breakfast
09:00-10:00
Reka Albert (Pennsylvania State University)
Qualitative modeling of gene regulatory networks
10:00-10:30
Break
10:30-11:30
Shayn Peirce-Cottler (University of Virginia)
Using Agent-Based Models to Study Tissue Patterning Processes: Linking Molecular Pathways to Multi-Cell Behaviors in Tissues
11:30-14:00
Lunch (on your own)

Afternoon Session

14:00-15:00
Claire Tomlin (University of California, Berkeley (UC Berkeley))
Using the adjoint method for parameter identification of large scale protein regulatory networks. Application to planar cell polarity in Drosophila.
15:00-15:30
Break
15:30-16:30
Hans Meinhardt (Max-Planck-Institut für Entwicklungsbiologie (Developmental Biology))
Self-poisoning of just established signalling centers - a common mechanism in biology to generate highly dynamic patterns
16:30-17:30
Armin Kaiser (Stanford University)
Evolution of multicellular complexity
17:30-19:00
Dinner (Hosted by IPAM)

Thursday, May 25, 2006

Morning Session

08:00-09:00
Continental Breakfast
09:00-10:00
Drew Endy (Massachusetts Institute of Technology)
Foundations for Engineering Biology
10:00-10:30
Break
10:30-11:30
Raymond Goldstein (University of Arizona)
Physical Aspects of Evolutionary Transitions to Multicellularity
11:30-13:15
Lunch (on your own)

Afternoon Session

13:15-14:00
William Smith (UC Santa Barbara)
Title not available
14:00-15:00
Ivet Bahar (University of Pittsburgh)
Network Models for Understanding Biomolecular Systems Dynamics and Allostery
15:00-15:30
Break
15:30-16:30
Richard Dickinson (University of Florida)
Models for Intracellular Particle Transport by Actin-Based Motility
16:30-17:30
Sean Sun (Johns Hopkins University)
Computational modeling of the cellular leading edge
17:30-18:30
James Glazier (Indiana University)
Demo of Cell Oriented Modeling Using Coppucell 3D

Friday, May 26, 2006

Morning Session

08:00-09:00
Continental Breakfast
09:00-10:00
Kevin Karplus (UC Santa Cruz)
Protein prediction: not another optimization problem
10:00-10:30
Break
10:30-11:30
David Stocum (Indiana University - Purdue University)
Self Organization of the Limb Regeneration Blastema: Cellular and Molecular Mechanisms
11:30-14:00
Lunch (on your own)

Afternoon Session

14:00-15:00
Gaudenz Danuser (The Scripps Research Institute)
Microtubule regulation by kinetochores: Experimental and numerical challenges
15:00-15:30
Break
15:30-16:30
Steven Gross (University of California, Irvine (UCI))
Title not available
16:30-17:30
Daniel Kamei (University of California, Los Angeles (UCLA))
Engineering Therapeutic Proteins with Cell-Level Modeling
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