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.

View FullText article

DOI, Mary Ann Liebert

Reviews [Write a review of this article]

There are no reviews of this article

Find related articles from these CiteULike users

tmmurali, ptrobajo, balicea, jiny, Borelli, longoka, Frontiers in Diabetes and Obesity (group)

Find related articles with these CiteULike tags

actex, cost, dragan, elementary, knockout, metabolic, metabolomics, methods, min_cutset, mode, network, networks, no-tag, reviews

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 = {cost, knockout, networks}, number = {3}, pages = {259--268}, posted-at = {2008-07-25 16:49:49}, 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 - cost KW - knockout KW - networks AU - Haus, Utz-Uwe AU - Klamt, Steffen AU - Stephen, Tamon PY - 2008/// UR - http://dx.doi.org/10.1089/cmb.2007.0229 ER -

RIS BibTeX