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Title: Computing the shortest elementary flux modes in genome-scale metabolic networks
Authors: de Figueiredo, LF
Podhorski, A
Rubio, A
Kaleta, C
Beasley, JE
Schuster, S
Planes, FJ
Keywords: Elementary flux modes;Metabolic networks;Integer linear programming;Escherichia coli;Corynebacterium glutamicum
Issue Date: 2009
Publisher: Oxford University Press
Citation: Bioinformatics, 25(23), 3158 - 3165, 2009
Abstract: Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size. Contact: Supplementary information: Supplementary data are available at Bioinformatics online (
Description: This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.
ISSN: 1367-4803
Appears in Collections:Dept of Mathematics Research Papers
Mathematical Sciences

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