Computing knock-out strategies in metabolic networks

Haus, U.-U.; Klamt, S.; Stephen, T.

doi:10.1089/cmb.2007.0229

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Computing knock-out strategies in metabolic networks

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Klamt, S.
Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Haus, U.-U., Klamt, S., & Stephen, T. (2008). Computing knock-out strategies in metabolic networks. Journal of Computational Biology, 15(3), 259-268. doi:10.1089/cmb.2007.0229.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0013-9637-B

Abstract

Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock-out sets of reactions required to block a given behavior. We describe an algorithm that improves the computation of these knock-out sets when the elementary modes (minimal functional subsystems) of the network are given. We also describe an algorithm that computes both the knock-out sets and the elementary modes containing the blocked reactions directly from the description of the network and whose worst-case computational complexity is better than the algorithms currently in use for these problems. Computational results are included. Copyright © Mary Ann Liebert, Inc. [accessed July 1, 2008]