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Analysis of biochemical networks using linear programming
SIMEONIDIS, Vangelis; Dartnell, Lewis; Bogle, I. David L. et al.
2005In Proceedings of the 7th World Congress of Chemical Engineering on CD-ROM
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Keywords :
linear programming; shortest path algorithm; pathway distance; metabolic pathways; genome distance; p53 cell cycle and apoptosis control network; network robustness; tumour inducing viruses
Abstract :
[en] The application of mathematical programming methodologies to biochemical systems is demonstrated with the presentation of a linear programming (LP) algorithm for calculating minimal pathway distances in biochemical networks. Minimal pathway distances are identified as the smallest number of steps separating two nodes in the network. Two case studies are examined: 1) the minimal distances for Escherichia coli Small Molecule Metabolism (SMM) enzymes are calculated and their correlations with genome distance and enzyme function are considered; 2) a study of the p53 cell cycle and apoptosis control network is performed in order to assess the survivability of the network to both random node failures and a directed assault, by studying the modification of the network’s diameter for successive protein knockouts. The results verify the applicability of the algorithm to problems of biochemical nature.
Disciplines :
Engineering, computing & technology: Multidisciplinary, general & others
Author, co-author :
SIMEONIDIS, Vangelis ;  University College London - UCL > Chemical Engineering
Dartnell, Lewis
Bogle, I. David L.
Papageorgiou, Lazaros G.
Language :
English
Title :
Analysis of biochemical networks using linear programming
Publication date :
December 2005
Event name :
7th World Congress of Chemical Engineering
Event organizer :
Institution of Chemical Engineers (IChemE)
Event place :
Glasgow (Scotland), United Kingdom
Event date :
10-14 July 2005
Audience :
International
Main work title :
Proceedings of the 7th World Congress of Chemical Engineering on CD-ROM
Publisher :
Institution of Chemical Engineers (IChemE)
ISBN/EAN :
9780852954942
Peer reviewed :
Peer reviewed
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since 11 June 2013

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