Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database

Bibliographic Details
Main Author: Oliveira, Alexandre Rafael Machado
Publication Date: 2022
Other Authors: Cunha, Emanuel Rodrigues, Cruz, Fernando João Pereira da, Ribeiro, João Manuel Capela Araújo, Costa, João Carlos Sequeira, Sampaio, Marta Sofia Costa, Dias, Oscar
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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network_name_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
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spelling 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
dc.type.driver.fl_str_mv conference paper
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
status_str 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
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 International Publishing AG
publisher.none.fl_str_mv Springer International Publishing AG
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
_version_ 1833595514328711168

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