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Summer Graduate School

MSRI Summer Graduate Workshop: Mathematical aspects of computational biology June 19, 2006 - June 30, 2006
Registration Deadline: June 01, 2006 almost 8 years ago
To apply for Funding you must register by: April 14, 2006 about 8 years ago
Organizers Reinhard Laubenbacher (Virginia Bioinformatics Institute at Virginia Tech) and Lior Pachter (Department of Mathematics, UC Berkeley)
Lecturer(s) No Lecturers Assigned Yet.
Speaker(s)

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Description 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.

Schedule
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Jun 19, 2006
Monday
09:00 AM - 10:00 AM
  Mathematical Aspects of Computational Biology
Reinhard Laubenbacher (Virginia Polytechnic Institute and State University)
02:00 PM - 03:00 PM
  A Segment Polarity Network in Drosophilia Melanogaster
Brandilyn Stigler
03:00 PM - 04:00 PM
  Discrete Modeling Paradigms
Reinhard Laubenbacher (Virginia Polytechnic Institute and State University)
Jun 20, 2006
Tuesday
09:00 AM - 10:00 AM
  Introduction to Reverse Engineering
Reinhard Laubenbacher (Virginia Polytechnic Institute and State University)
10:30 AM - 11:30 AM
  Introduction to Computational Algebra
Reinhard Laubenbacher (Virginia Polytechnic Institute and State University)
02:00 PM - 03:00 PM
  Software PAckages for Computational Biology
Brandilyn Stigler
Jun 21, 2006
Wednesday
09:00 AM - 10:00 AM
  Reverse Engineering of Networks
Reinhard Laubenbacher (Virginia Polytechnic Institute and State University)
02:00 PM - 03:00 PM
  Reverse Engineering the Segment Polarity Network
Brandilyn Stigler
Jun 22, 2006
Thursday
09:00 AM - 10:00 AM
  Algebraic Statistics for Computational Biology
10:30 AM - 11:30 AM
  Parametic Alignment and Conservation of Cis-Regulatory Elements
02:00 PM - 03:00 PM
  Robustness of Spatial Patterning
Hans Othmer
Jun 23, 2006
Friday
09:00 AM - 10:00 AM
  Introduction to the Mathematics of Phylogenomics
02:00 PM - 03:00 PM
  Talk- Mathematical Aspects of Computational Biology
Jun 24, 2006
Saturday
10:30 AM - 11:30 AM
  Talk- Mathematical Aspects of Computational Biology
Jun 26, 2006
Monday
09:00 AM - 10:00 AM
  Talk- Mathematical Aspects of Computational Biology
02:00 PM - 03:00 PM
  Epistasis and Shapes of Fitness and Landscapes
03:30 PM - 04:30 PM
  Evolution on Distributive Lattices
Nicholas Eriksson
Jun 27, 2006
Tuesday
09:00 AM - 10:00 AM
  Talk- Mathematical Aspects of Computational Biology
Jason Morton (Pennsylvania State University)
02:00 PM - 03:00 PM
  Talk- Mathematical Aspects of Computational Biology
Ariel Schwartz
Jun 28, 2006
Wednesday
02:00 PM - 03:00 PM
  Talk- Mathematical Aspects of Computational Biology
Jun 29, 2006
Thursday
09:00 AM - 10:00 AM
  Group work- Mathematical Aspects of Computational Biology
10:30 AM - 11:30 AM
  Group work- Mathematical Aspects of Computational Biology
02:00 PM - 03:30 PM
  Grobner Bases
Bernd Sturmfels (UC Berkeley Math Faculty)
Jun 30, 2006
Friday
09:00 AM - 10:00 AM
  Longest Identity Sequence
Yu Huang
10:00 AM - 11:00 AM
  Talk- Mathematical Aspects of Computational Biology
Oliver Wienand
11:00 AM - 12:00 PM
  Talk- Mathematical Aspects of Computational Biology
Oliver Wienand
12:00 PM - 12:30 PM
  Talk- Mathematical Aspects of Computational Biology
Michael Mehan