Journal Article

An optimization model for metabolic pathways

F. J. Planes and J. E. Beasley

in Bioinformatics

Volume 25, issue 20, pages 2723-2729
Published in print October 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp441
An optimization model for metabolic pathways

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Motivation: Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner.

Contact: john.beasley@brunel.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6406 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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