Comparison of pathway analysis and constraint-based methods for cell factory design

Detalhes bibliográficos
Autor(a) principal: Vieira, Vítor
Data de Publicação: 2019
Outros Autores: Maia, Paulo, Rocha, Miguel, Rocha, I.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/60616
Resumo: Computational strain optimisation methods (CSOMs) have been successfully used to exploit genome-scale metabolic models, yielding strategies useful for allowing compound overproduction in metabolic cell factories. Minimal cut sets are particularly interesting since their definition allows searching for intervention strategies that impose strong growth-coupling phenotypes, and are not subject to optimality bias when compared with simulation-based CSOMs. However, since both types of methods have different underlying principles, they also imply different ways to formulate metabolic engineering problems, posing an obstacle when comparing their outputs.
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spelling Comparison of pathway analysis and constraint-based methods for cell factory designGenome-scale metabolic modelsComputational strain designMetabolic pathway analysisEvolutionary algorithmsMinimal cut setsGrowth-coupled product synthesisCiências Médicas::Biotecnologia MédicaCiências Naturais::Ciências da Computação e da InformaçãoScience & TechnologyComputational strain optimisation methods (CSOMs) have been successfully used to exploit genome-scale metabolic models, yielding strategies useful for allowing compound overproduction in metabolic cell factories. Minimal cut sets are particularly interesting since their definition allows searching for intervention strategies that impose strong growth-coupling phenotypes, and are not subject to optimality bias when compared with simulation-based CSOMs. However, since both types of methods have different underlying principles, they also imply different ways to formulate metabolic engineering problems, posing an obstacle when comparing their outputs.“DeYeastLibrary – Designer yeast strain library optimized for metabolic engineering applications”, Ref.ERA-IB-2/0003/2013, funded by national funds through FCT/MCTES, DD-DeCaf and SHIKIFACTORY100, both funded by the European Union through the Horizon 2020 research and innovation programme (grant agreements no. 686070 and 814408). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 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. The authors acknowledge the use of computing facilities within the scope of the Search-ON2: Revitalization of HPC infrastructure of UMinho” project (NORTE-07-0162-FEDER-000086), co-funded by the North Portugal Regional Operational Programme (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF). VV also thanks funding from FCT/MCTES for the PhD studentship with reference SFRH/BD/118657/2016.info:eu-repo/semantics/publishedVersionSpringer NatureUniversidade do MinhoVieira, VítorMaia, PauloRocha, MiguelRocha, I.2019-06-202019-06-20T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/60616engVieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel, Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics, 20(350), 20191471-21051471-210510.1186/s12859-019-2934-y31221092https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2934-yinfo: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:RCAAP2023-07-21T12:39:21Zoai:repositorium.sdum.uminho.pt:1822/60616Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:35:57.728978Repositório 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 Comparison of pathway analysis and constraint-based methods for cell factory design
title Comparison of pathway analysis and constraint-based methods for cell factory design
spellingShingle Comparison of pathway analysis and constraint-based methods for cell factory design
Vieira, Vítor
Genome-scale metabolic models
Computational strain design
Metabolic pathway analysis
Evolutionary algorithms
Minimal cut sets
Growth-coupled product synthesis
Ciências Médicas::Biotecnologia Médica
Ciências Naturais::Ciências da Computação e da Informação
Science & Technology
title_short Comparison of pathway analysis and constraint-based methods for cell factory design
title_full Comparison of pathway analysis and constraint-based methods for cell factory design
title_fullStr Comparison of pathway analysis and constraint-based methods for cell factory design
title_full_unstemmed Comparison of pathway analysis and constraint-based methods for cell factory design
title_sort Comparison of pathway analysis and constraint-based methods for cell factory design
author Vieira, Vítor
author_facet Vieira, Vítor
Maia, Paulo
Rocha, Miguel
Rocha, I.
author_role author
author2 Maia, Paulo
Rocha, Miguel
Rocha, I.
author2_role author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Vieira, Vítor
Maia, Paulo
Rocha, Miguel
Rocha, I.
dc.subject.por.fl_str_mv Genome-scale metabolic models
Computational strain design
Metabolic pathway analysis
Evolutionary algorithms
Minimal cut sets
Growth-coupled product synthesis
Ciências Médicas::Biotecnologia Médica
Ciências Naturais::Ciências da Computação e da Informação
Science & Technology
topic Genome-scale metabolic models
Computational strain design
Metabolic pathway analysis
Evolutionary algorithms
Minimal cut sets
Growth-coupled product synthesis
Ciências Médicas::Biotecnologia Médica
Ciências Naturais::Ciências da Computação e da Informação
Science & Technology
description Computational strain optimisation methods (CSOMs) have been successfully used to exploit genome-scale metabolic models, yielding strategies useful for allowing compound overproduction in metabolic cell factories. Minimal cut sets are particularly interesting since their definition allows searching for intervention strategies that impose strong growth-coupling phenotypes, and are not subject to optimality bias when compared with simulation-based CSOMs. However, since both types of methods have different underlying principles, they also imply different ways to formulate metabolic engineering problems, posing an obstacle when comparing their outputs.
publishDate 2019
dc.date.none.fl_str_mv 2019-06-20
2019-06-20T00:00:00Z
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/1822/60616
url http://hdl.handle.net/1822/60616
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel, Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics, 20(350), 2019
1471-2105
1471-2105
10.1186/s12859-019-2934-y
31221092
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2934-y
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 Springer Nature
publisher.none.fl_str_mv Springer Nature
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
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