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

Detalhes bibliográficos
Autor(a) principal: Cruz, Fernando
Data de Publicação: 2020
Outros Autores: Faria, José Pedro, Rocha, Miguel, Rocha, Isabel, Dias, Oscar
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/74304
Resumo: The 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.
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spelling A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulationFlux balance analysisGene expression and regulationGenome-scale metabolic modelsGenome-scale regulatory networksMetabolismTranscriptional regulatory networksEngenharia e Tecnologia::Biotecnologia IndustrialScience & TechnologyThe 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.This 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.info:eu-repo/semantics/publishedVersionPortland PressUniversidade do MinhoCruz, FernandoFaria, José PedroRocha, MiguelRocha, IsabelDias, Oscar2020-09-172020-09-17T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/74304engCruz, 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), 1889-19030300-512710.1042/bst2019084032940659https://portlandpress.com/biochemsoctrans/article-abstract/48/5/1889/226439/A-review-of-methods-for-the-reconstruction-and?redirectedFrom=fulltextinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:28:43Zoai:repositorium.sdum.uminho.pt:1822/74304Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:23:35.246401Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
title A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
spellingShingle A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
Cruz, Fernando
Flux balance analysis
Gene expression and regulation
Genome-scale metabolic models
Genome-scale regulatory networks
Metabolism
Transcriptional regulatory networks
Engenharia e Tecnologia::Biotecnologia Industrial
Science & Technology
title_short A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
title_full A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
title_fullStr A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
title_full_unstemmed A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
title_sort A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
author Cruz, Fernando
author_facet Cruz, Fernando
Faria, José Pedro
Rocha, Miguel
Rocha, Isabel
Dias, Oscar
author_role author
author2 Faria, José Pedro
Rocha, Miguel
Rocha, Isabel
Dias, Oscar
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Cruz, Fernando
Faria, José Pedro
Rocha, Miguel
Rocha, Isabel
Dias, Oscar
dc.subject.por.fl_str_mv Flux balance analysis
Gene expression and regulation
Genome-scale metabolic models
Genome-scale regulatory networks
Metabolism
Transcriptional regulatory networks
Engenharia e Tecnologia::Biotecnologia Industrial
Science & Technology
topic Flux balance analysis
Gene expression and regulation
Genome-scale metabolic models
Genome-scale regulatory networks
Metabolism
Transcriptional regulatory networks
Engenharia e Tecnologia::Biotecnologia Industrial
Science & Technology
description The 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.
publishDate 2020
dc.date.none.fl_str_mv 2020-09-17
2020-09-17T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1822/74304
url http://hdl.handle.net/1822/74304
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Cruz, 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), 1889-1903
0300-5127
10.1042/bst20190840
32940659
https://portlandpress.com/biochemsoctrans/article-abstract/48/5/1889/226439/A-review-of-methods-for-the-reconstruction-and?redirectedFrom=fulltext
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Portland Press
publisher.none.fl_str_mv Portland Press
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799132711638532096

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