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dc.contributor.authorKrieger, S.
dc.contributor.authorKececioglu, J.
dc.date.accessioned2022-07-08T22:27:20Z
dc.date.available2022-07-08T22:27:20Z
dc.date.issued2022
dc.identifier.citationKrieger, S., & Kececioglu, J. (2022). Computing optimal factories in metabolic networks with negative regulation. Bioinformatics (Oxford, England), 38(1), i369–i377.
dc.identifier.issn1367-4811
dc.identifier.pmid35758789
dc.identifier.doi10.1093/bioinformatics/btac231
dc.identifier.urihttp://hdl.handle.net/10150/665350
dc.description.abstractMOTIVATION: A factory in a metabolic network specifies how to produce target molecules from source compounds through biochemical reactions, properly accounting for reaction stoichiometry to conserve or not deplete intermediate metabolites. While finding factories is a fundamental problem in systems biology, available methods do not consider the number of reactions used, nor address negative regulation. METHODS: We introduce the new problem of finding optimal factories that use the fewest reactions, for the first time incorporating both first- and second-order negative regulation. We model this problem with directed hypergraphs, prove it is NP-complete, solve it via mixed-integer linear programming, and accommodate second-order negative regulation by an iterative approach that generates next-best factories. RESULTS: This optimization-based approach is remarkably fast in practice, typically finding optimal factories in a few seconds, even for metabolic networks involving tens of thousands of reactions and metabolites, as demonstrated through comprehensive experiments across all instances from standard reaction databases. AVAILABILITY AND IMPLEMENTATION: Source code for an implementation of our new method for optimal factories with negative regulation in a new tool called Odinn, together with all datasets, is available free for non-commercial use at http://odinn.cs.arizona.edu. © The Author(s) 2022. Published by Oxford University Press.
dc.language.isoen
dc.publisherOxford Academic
dc.rightsCopyright © The Author(s) 2022. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleComputing optimal factories in metabolic networks with negative regulation
dc.typeArticle
dc.typetext
dc.contributor.departmentDepartment of Computer Science, University of Arizona
dc.identifier.journalBioinformatics (Oxford, England)
dc.description.noteOpen access article
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
dc.eprint.versionFinal published version
dc.source.journaltitleBioinformatics (Oxford, England)
refterms.dateFOA2022-07-08T22:27:20Z


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Copyright © The Author(s) 2022. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
Except where otherwise noted, this item's license is described as Copyright © The Author(s) 2022. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).