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Summer Graduate Workshop
MSRI Summer Graduate Workshop: Mathematical aspects of computational biology
Jun 19, 2006 to Jun 30, 2006

Organizer(s)

Reinhard Laubenbacher (Virginia Bioinformatics Institute at Virginia Tech) and Lior Pachter (Department of Mathematics, UC Berkeley)

Contact

This workshop will be specifically focused on the mathematical aspects of computational biology.

Workshop Schedule

Topics
We need a hierarchy of scales to understand and integrate the knowledge gained from the landmark undertaking of mapping the human genome sequence. Understanding of how the vast variety of biochemical compounds, including proteins and metabolites, interact with each other and form complex reaction networks is the next step. These networks comprise the complex cellular interaction networks of cell metabolism. Organism and population scales above these require yet different analysis tools.

In this workshop we will focus on the first two scales: the genome and intracellular biochemical reaction networks, including gene regulatory networks. The course will be organized around the following datasets:
  • The yeast genome(s)

  • The human genome, completed and finished to high quality in 2004

  • Time series of yeast DNA microarray measurements, including a control and response to oxidative stress, generated at VBI

Workshop activities involving these data sets are as follows:
  • Find orthologs and homologs to yeast genes involved in oxidative stress response in the human genome, in order to find candidate genes for an oxidative stress response network in human tissue

  • Create mathematical models of network dynamics for the yeast oxidative stress network, using several modeling methodologies from both continuous and discrete mathematics

The workshop will provide background lectures in Biology and Mathematics.

Priority for this workshop is given to graduate students at MSRI Academic Sponsoring Institutions. If you are at one of these institutions, request your Director of Graduate Studies to nominate you. After these nominations are in, applicants will be considered for admission and possible funding, if such funding is still available. These considerations will take place before April 15, 2006.

Important

Schedule
Monday, June 19, 2006
9:00AM - 10:00AM Reinhard Laubenbacher Mathematical Aspects of Computational Biology [Video available]
2:00PM - 3:00PM Brandilyn Stigler A Segment Polarity Network in Drosophilia Melanogaster [Video available]
3:00PM - 4:00PM Reinhard Laubenbacher Discrete Modeling Paradigms [Video available]
Tuesday, June 20, 2006
9:00AM - 10:00AM Reinhard Laubenbacher Introduction to Reverse Engineering [Video available]
10:30AM - 11:30AM Reinhard Laubenbacher Introduction to Computational Algebra [Video available]
2:00PM - 3:00PM Brandilyn Stigler Software PAckages for Computational Biology [Video available]
Wednesday, June 21, 2006
9:00AM - 10:00AM Reinhard Laubenbacher Reverse Engineering of Networks [Video available]
2:00PM - 3:00PM Brandilyn Stigler Reverse Engineering the Segment Polarity Network [Video available]
Thursday, June 22, 2006
9:00AM - 10:00AM Algebraic Statistics for Computational Biology [Video available]
10:30AM - 11:30AM Parametic Alignment and Conservation of Cis-Regulatory Elements [Video available]
2:00PM - 3:00PM Hans Othmer Robustness of Spatial Patterning [Video available]
Friday, June 23, 2006
9:00AM - 10:00AM Introduction to the Mathematics of Phylogenomics [Video available]
2:00PM - 3:00PM Talk- Mathematical Aspects of Computational Biology [Video available]
Saturday, June 24, 2006
10:30AM - 11:30AM Talk- Mathematical Aspects of Computational Biology [Video available]
Monday, June 26, 2006
9:00AM - 10:00AM Talk- Mathematical Aspects of Computational Biology [Video available]
2:00PM - 3:00PM Epistasis and Shapes of Fitness and Landscapes [Video available]
3:30PM - 4:30PM Nicholas Eriksson Evolution on Distributive Lattices [Video available]
Tuesday, June 27, 2006
9:00AM - 10:00AM Jason Morton Talk- Mathematical Aspects of Computational Biology [Video available]
2:00PM - 3:00PM Ariel Schwartz Talk- Mathematical Aspects of Computational Biology [Video available]
Wednesday, June 28, 2006
2:00PM - 3:00PM Talk- Mathematical Aspects of Computational Biology [Video available]
Thursday, June 29, 2006
9:00AM - 10:00AM , Group work- Mathematical Aspects of Computational Biology
10:30AM - 11:30AM Group work- Mathematical Aspects of Computational Biology [Video available]
2:00PM - 3:30PM Bernd Sturmfels Grobner Bases [Video available]
Friday, June 30, 2006
9:00AM - 10:00AM Yu Huang Longest Identity Sequence [Video available]
10:00AM - 11:00AM Oliver Wienand Talk- Mathematical Aspects of Computational Biology [Video available]
11:00AM - 12:00PM Oliver Wienand Talk- Mathematical Aspects of Computational Biology [Video available]
12:00PM - 12:30PM Michael Mehan Talk- Mathematical Aspects of Computational Biology [Video available]


Questions about this workshop should be sent either by email to
330@msri.org

or by regular mail to:
MSRI Summer Graduate Workshop: Mathematical aspects of computational biology
Mathematical Sciences Research Institute
17 Gauss Way, Berkeley, CA
94720-5070.
USA

The Institute is committed to the principles of Equal Opportunity and Affirmative Action.



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