Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database
| Main Author: | |
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| Publication Date: | 2022 |
| Other Authors: | , , , , , |
| Language: | eng |
| Source: | Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) |
| Download full: | https://hdl.handle.net/1822/74708 |
Summary: | First Online: 28 August 2021 |
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Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models databaseGenome-scale metabolic modelsMerlin BiGG integration toolBiGG modelsMerlinBiGG Integration ToolScience & TechnologyFirst Online: 28 August 2021Genome-Scale metabolic models (GEMs) are a relevant tool in systems biology for in silico strain optimisation and drug discovery. An easier way to reconstruct a model is to use available GEMs as templates to create the initial draft, which can be curated up until a simulation-ready model is obtained. This approach is implemented in merlin's BiGG Integration Tool, which reconstructs models from existing GEMs present in the BiGG Models database. This study aims to assess draft models generated using models from BiGG as templates for three distinct organisms, namely, Streptococcus thermophilus, Xylella fastidiosa and Mycobacterium tuberculosis. Several draft models were reconstructed using the BiGG Integration Tool and different templates (all, selected and random). The variability of the models was assessed using the reactions and metabolic functions associated with the model's genes. This analysis showed that, even though the models shared a significant portion of reactions and metabolic functions, models from different organisms are still differentiated. Moreover, there also seems to be variability among the templates used to generate the draft models to a lower extent. This study concluded that the BiGG Integration Tool provides a fast and reliable alternative for draft reconstruction for bacteria.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. A. Oliveira (DFA/BD/10205/2020), E. Cunha (DFA/BD/8076/2020), F. Cruz (SFRH /BD/139198/2018), J. Sequeira (SFRH/BD/147271/2019), and M. Sampaio (SFRH/BD/144643/2019) hold a doctoral fellowship provided by the FCT. Oscar Dias acknowledge FCT for the Assistant Research contract obtained under CEEC Individual 2018.info:eu-repo/semantics/publishedVersionSpringer International Publishing AGUniversidade do MinhoOliveira, Alexandre Rafael MachadoCunha, Emanuel RodriguesCruz, Fernando João Pereira daRibeiro, João Manuel Capela AraújoCosta, João Carlos SequeiraSampaio, Marta Sofia CostaDias, Oscar20222022-01-01T00:00:00Zconference paperinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/1822/74708engOliveira, Alexandre; Cunha, Emanuel; Cruz, Fernando; Ribeiro, João; Sequeira, J. C.; Sampaio, Marta; Dias, Oscar (2022). Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database. In: Rocha, M., Fdez-Riverola, F., Mohamad, M.S., Casado-Vara, R. (eds) Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021). PACBB 2021. Lecture Notes in Networks and Systems, vol 325. Springer, Cham. https://doi.org/10.1007/978-3-030-86258-9_14978-3-030-86258-92367-337010.1007/978-3-030-86258-9_14978-3-030-86258-9https://link.springer.com/chapter/10.1007/978-3-030-86258-9_14info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-11T06:12:30Zoai:repositorium.sdum.uminho.pt:1822/74708Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T15:44:42.938818Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse |
| dc.title.none.fl_str_mv |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| title |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| spellingShingle |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database Oliveira, Alexandre Rafael Machado Genome-scale metabolic models Merlin BiGG integration tool BiGG models Merlin BiGG Integration Tool Science & Technology |
| title_short |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| title_full |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| title_fullStr |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| title_full_unstemmed |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| title_sort |
Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database |
| author |
Oliveira, Alexandre Rafael Machado |
| author_facet |
Oliveira, Alexandre Rafael Machado Cunha, Emanuel Rodrigues Cruz, Fernando João Pereira da Ribeiro, João Manuel Capela Araújo Costa, João Carlos Sequeira Sampaio, Marta Sofia Costa Dias, Oscar |
| author_role |
author |
| author2 |
Cunha, Emanuel Rodrigues Cruz, Fernando João Pereira da Ribeiro, João Manuel Capela Araújo Costa, João Carlos Sequeira Sampaio, Marta Sofia Costa Dias, Oscar |
| author2_role |
author author author author author author |
| dc.contributor.none.fl_str_mv |
Universidade do Minho |
| dc.contributor.author.fl_str_mv |
Oliveira, Alexandre Rafael Machado Cunha, Emanuel Rodrigues Cruz, Fernando João Pereira da Ribeiro, João Manuel Capela Araújo Costa, João Carlos Sequeira Sampaio, Marta Sofia Costa Dias, Oscar |
| dc.subject.por.fl_str_mv |
Genome-scale metabolic models Merlin BiGG integration tool BiGG models Merlin BiGG Integration Tool Science & Technology |
| topic |
Genome-scale metabolic models Merlin BiGG integration tool BiGG models Merlin BiGG Integration Tool Science & Technology |
| description |
First Online: 28 August 2021 |
| publishDate |
2022 |
| dc.date.none.fl_str_mv |
2022 2022-01-01T00:00:00Z |
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conference paper |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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publishedVersion |
| dc.identifier.uri.fl_str_mv |
https://hdl.handle.net/1822/74708 |
| url |
https://hdl.handle.net/1822/74708 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
Oliveira, Alexandre; Cunha, Emanuel; Cruz, Fernando; Ribeiro, João; Sequeira, J. C.; Sampaio, Marta; Dias, Oscar (2022). Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database. In: Rocha, M., Fdez-Riverola, F., Mohamad, M.S., Casado-Vara, R. (eds) Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021). PACBB 2021. Lecture Notes in Networks and Systems, vol 325. Springer, Cham. https://doi.org/10.1007/978-3-030-86258-9_14 978-3-030-86258-9 2367-3370 10.1007/978-3-030-86258-9_14 978-3-030-86258-9 https://link.springer.com/chapter/10.1007/978-3-030-86258-9_14 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
| dc.publisher.none.fl_str_mv |
Springer International Publishing AG |
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Springer International Publishing AG |
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reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia instacron:RCAAP |
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