A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

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dc.commentsCEB53909por
dc.contributor.authorCruz, Fernandopor
dc.contributor.authorFaria, José Pedropor
dc.contributor.authorRocha, Miguelpor
dc.contributor.authorRocha, Isabelpor
dc.contributor.authorDias, Oscarpor
dc.date.accessioned2021-10-11T11:07:08Z
dc.date.available2021-10-11T11:07:08Z
dc.date.issued2020-09-17
dc.date.updated2021-10-09T11:52:17Z
dc.description.abstractThe current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.por
dc.description.publicationversioninfo:eu-repo/semantics/publishedVersion
dc.description.sponsorshipThis study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04 469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 -Programa Operacional Regional do Norte. Fernando Cruz holds a doctoral fellowship (SFRH/BD/139198/2018) funded by the FCT. This study was supported by the European Commission through project SHIKIFACTORY100 -Modular cell factories for the production of 100 compounds from the shikimate pathway (Reference 814408). The submitted manuscript has been created by UChicago Argonne, LLC as Operator of Argonne National Laboratory (`Argonne') under Contract No. DE-AC02-06CH11357 with the U.S. Department of Energy. The U.S. Government retains for itself, and others acting on its behalf, a paid-up, nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan.por
dc.distributioninternationalpor
dc.identifier.citationCruz, F., Faria, J. P., Rocha, M., Rocha, I., & Dias, O. (2020). A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation. Biochemical Society Transactions, 48(5), 1889-1903por
dc.identifier.doi10.1042/bst20190840por
dc.identifier.issn0300-5127por
dc.identifier.pmid32940659por
dc.identifier.urihttps://hdl.handle.net/1822/74304
dc.language.isoengpor
dc.peerreviewedyespor
dc.publisherPortland Presspor
dc.relation.publisherversionhttps://portlandpress.com/biochemsoctrans/article-abstract/48/5/1889/226439/A-review-of-methods-for-the-reconstruction-and?redirectedFrom=fulltextpor
dc.rightsopenAccesspor
dc.subjectFlux balance analysispor
dc.subjectGene expression and regulationpor
dc.subjectGenome-scale metabolic modelspor
dc.subjectGenome-scale regulatory networkspor
dc.subjectMetabolismpor
dc.subjectTranscriptional regulatory networkspor
dc.subject.fosEngenharia e Tecnologia::Biotecnologia Industrialpor
dc.subject.wosScience & Technologypor
dc.titleA review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulationpor
dc.typearticle
dspace.entity.typePublicationen
oaire.citationConferencePlaceUnited Kingdom
oaire.citationEndPage1903por
oaire.citationIssueBST20190840por
oaire.citationStartPage1889por
oaire.citationVolume2020por
sdum.journalBiochemical Society Transactionspor

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