Computing elementary flux modes involving a set of target reactions

Please always quote using this URN:urn:nbn:de:0296-matheon-12621
  • Elementary flux mode (EM) analysis is an important tool in the constraint-based analysis of genome-scale metabolic networks. Due to the combinatorial complexity of these networks, as well as the advances in the level of detail to which they can be reconstructed, an exhaustive enumeration of all EMs is often not practical. Therefore, in recent years interest has shifted towards searching EMs with specific properties. We present a novel method that allows computing EMs containing a given set of target reactions. This generalizes previous algorithms where the set of target reactions consists of a single reaction. In the one-reaction case, our method compares favorably to the previous approaches. In addition, we present several applications of our algorithm for computing EMs containing two target reactions in genome-scale metabolic networks.

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Author:Laszlo David, Alexander Bockmayr
Referee:Peter Deuflhard
Document Type:Preprint, Research Center Matheon
Date of first Publication:2013/11/29
Release Date:2013/11/29
Tag:constraint-based analysis; metabolic networks; elementary flux modes
Institute:Research Center Matheon
Freie Universität Berlin
MSC-Classification:92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C42 Systems biology, networks
Preprint Number:1045
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