Molecular Networks Decomposition and the Computation of Elementary Modes
Speaker: Julien Gagneur , EMBLContact:
Date: March 27 2006
Time: 11:30AM to 1:00PM
Location: TOC lab 32-G575
Host: P Clote/ BC & B Berger/ MIT
Kathleen Dickey, 617 253 3037, email@example.comRelevant URL: http://www-math.mit.edu/compbiosem/
Molecular networks provide the structure of dynamic systems driving
cell biology. Systematic application of current technologies and
genome annotation have enabled the construction of large networks of
protein interactions and metabolic networks for several model
organisms. These resulting molecular networks are large and complex
and their large-scale analysis poses several computational challenges.
In this talk, I will first focus on decomposition techniques that
facilitate the analysis of molecular networks by dividing them into
subnetworks. I will show a method that decomposes metabolic networks
into independent parts and its application to E.coli metabolism.
Another method, named modular decomposition, applies to protein
interaction networks and derives the logical rules that proteins
follow to assemble and form particular protein complexes. Modular
decomposition is applied to the human TNF-alpha signaling pathway.
The second part of the talk focuses on the computation of elementary
modes, which are minimal functional units in a metabolic network. This
question is equivalent to the classical vertex enumeration problem
from combinatorial geometry. However, state-of-the-art methods are
limited in practice when dealing with large networks. I will show
practical improvements of the algorithm and address the issue of
Department of Mathematics
& The Theory of
The seminar is co-hosted by Professor Peter Clote of Boston College's Biology and Computer Science Departments and MIT Professor of Applied Math Bonnie Berger. Professor Berger is also affiliated with CSAIL & HST.
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