Genome-scale modeling of yeast: chronology, applications and critical perspectives

Detalhes bibliográficos
Autor(a) principal: Lopes, Hélder
Data de Publicação: 2017
Outros Autores: Rocha, Isabel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/47490
Resumo: Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed
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spelling Genome-scale modeling of yeast: chronology, applications and critical perspectivesyeastgenome-scale metabolic modelmetabolismconstraint-based modellingmetabolic engineeringcell factoryconstraint-based modelingScience & TechnologyOver the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressedThis work was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of a Ph.D. grant (PD/BD/52336/2013), of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01–0145FEDER-006684) and also in the context of the EU-funded initiative ERA-NET for Industrial Biotechnology (ERA-IB-2/0003/2013), in addition to the BioTecNorte operation (NORTE-01–0145FEDER-000004) funded by European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersionOxford University PressUniversidade do MinhoLopes, HélderRocha, Isabel2017-082017-08-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/47490engLopes, Hélder; Rocha, Isabel, Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Research, 17(5), fox050, 20171567-13641567-13561567-136410.1093/femsyr/fox05028899034http://femsyr.oxfordjournals.org/info: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:RCAAP2023-07-21T12:22:49Zoai:repositorium.sdum.uminho.pt:1822/47490Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:16:22.701820Repositório 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 Genome-scale modeling of yeast: chronology, applications and critical perspectives
title Genome-scale modeling of yeast: chronology, applications and critical perspectives
spellingShingle Genome-scale modeling of yeast: chronology, applications and critical perspectives
Lopes, Hélder
yeast
genome-scale metabolic model
metabolism
constraint-based modelling
metabolic engineering
cell factory
constraint-based modeling
Science & Technology
title_short Genome-scale modeling of yeast: chronology, applications and critical perspectives
title_full Genome-scale modeling of yeast: chronology, applications and critical perspectives
title_fullStr Genome-scale modeling of yeast: chronology, applications and critical perspectives
title_full_unstemmed Genome-scale modeling of yeast: chronology, applications and critical perspectives
title_sort Genome-scale modeling of yeast: chronology, applications and critical perspectives
author Lopes, Hélder
author_facet Lopes, Hélder
Rocha, Isabel
author_role author
author2 Rocha, Isabel
author2_role author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Lopes, Hélder
Rocha, Isabel
dc.subject.por.fl_str_mv yeast
genome-scale metabolic model
metabolism
constraint-based modelling
metabolic engineering
cell factory
constraint-based modeling
Science & Technology
topic yeast
genome-scale metabolic model
metabolism
constraint-based modelling
metabolic engineering
cell factory
constraint-based modeling
Science & Technology
description Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed
publishDate 2017
dc.date.none.fl_str_mv 2017-08
2017-08-01T00:00:00Z
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/1822/47490
url http://hdl.handle.net/1822/47490
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Lopes, Hélder; Rocha, Isabel, Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Research, 17(5), fox050, 2017
1567-1364
1567-1356
1567-1364
10.1093/femsyr/fox050
28899034
http://femsyr.oxfordjournals.org/
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 Oxford University Press
publisher.none.fl_str_mv Oxford University 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
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