Computing Knock-Out Strategies in Metabolic Networks

by: Utz-Uwe Haus, Steffen Klamt, Tamon Stephen

Journal of Computational Biology, Vol. 15, No. 3. (2008), pp. 259-268.

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DOI, Mary Ann Liebert

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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.

@article{citeulike:2609210, 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.}, author = {Haus, Utz-Uwe and Klamt, Steffen and Stephen, Tamon }, citeulike-article-id = {2609210}, doi = {http://dx.doi.org/10.1089/cmb.2007.0229}, journal = {Journal of Computational Biology}, keywords = {min\_cutset}, number = {3}, pages = {259--268}, posted-at = {2008-07-25 16:22:22}, priority = {2}, title = {Computing Knock-Out Strategies in Metabolic Networks}, url = {http://dx.doi.org/10.1089/cmb.2007.0229}, volume = {15}, year = {2008} }

RIS record

TY - JOUR ID - citeulike:2609210 L3 - citeulike-article-id:2609210 TI - Computing Knock-Out Strategies in Metabolic Networks JF - Journal of Computational Biology VL - 15 IS - 3 SP - 259 EP - 268 N2 - 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. KW - min_cutset AU - Haus, Utz-Uwe AU - Klamt, Steffen AU - Stephen, Tamon PY - 2008/// UR - http://dx.doi.org/10.1089/cmb.2007.0229 ER -

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