FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria

Bibliographic Details
Main Author: Merigueti, Thiago Castanheira
Publication Date: 2019
Other Authors: Carneiro, Marcia Weber, Carvalho-Assef, Ana Paula d' A., Silva Jr, Floriano Paes, Silva, Fabricio Alves Barbosa da
Format: Article
Language: eng
Source: Repositório Institucional da FIOCRUZ (ARCA)
DOI: 10.3389/fgene.2019.00633
Download full: https://arca.fiocruz.br/handle/icict/33899
Summary: CAPES, FAPERJ, CNPq e FIOCRUZ (INOVA-FIOCRUZ VPPCB-007-FIO-18-2-29) for financial support.
id CRUZ_cc3e8af00afb5455174654129e80f07c
oai_identifier_str oai:arca.fiocruz.br:icict/33899
network_acronym_str CRUZ
network_name_str Repositório Institucional da FIOCRUZ (ARCA)
repository_id_str 2135
spelling Merigueti, Thiago CastanheiraCarneiro, Marcia WeberCarvalho-Assef, Ana Paula d' A.Silva Jr, Floriano PaesSilva, Fabricio Alves Barbosa da2019-07-09T11:45:07Z2019-07-09T11:45:07Z2019MERIGUETI, Thiago Castanheira et al. FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. Frontiers in Genetics, v. 10, p. 1-14, July 2019.1664-8021https://arca.fiocruz.br/handle/icict/3389910.3389/fgene.2019.00633CAPES, FAPERJ, CNPq e FIOCRUZ (INOVA-FIOCRUZ VPPCB-007-FIO-18-2-29) for financial support.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Muniz. Programa de Pós-Graduação em Biotecnologia para Saúde e Medicina Investigativa. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Bioquímica Experimental e Computacional de Fármacos. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ. Brasil.Healthcare-associated infections (HAIs) are a serious public health problem. They can be associated with morbidity and mortality and are responsible for the increase in patient hospitalization. Antimicrobial resistance among pathogens causing HAI has increased at alarming levels. In this paper, a robust method for analyzing genome-scale metabolic networks of bacteria is proposed in order to identify potential therapeutic targets, along with its corresponding web implementation, dubbed FindTargetsWEB. The proposed method assumes that every metabolic network presents fragile genes whose blockade will impair one or more metabolic functions, such as biomass accumulation. FindTargetsWEB automates the process of identification of such fragile genes using flux balance analysis (FBA), flux variability analysis (FVA), extended Systems Biology Markup Language (SBML) file parsing, and queries to three public repositories, i.e., KEGG, UniProt, and DrugBank. The web application was developed in Python using COBRApy and Django.engFrontiers MediaBiologia de sistemasAnálise de Balanço de FluxoRede MetabólicaAnálise COBRAPython (linguagem de programação)Systems biologyFlux balance analysisMetabolic networkCOBRA analysisPython (programming language)FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteriainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://arca.fiocruz.br/bitstreams/8a97e365-9bf1-4ee6-bb7b-603b5aa7e6ba/download5a560609d32a3863062d77ff32785d58MD51falseAnonymousREADORIGINALAnaPaulaC_Assef_etal_IOC_2019.pdfAnaPaulaC_Assef_etal_IOC_2019.pdfapplication/pdf1229680https://arca.fiocruz.br/bitstreams/2b8c1693-fa75-49ea-82f1-f43dc897096a/download3f189d37debf3938623bdbf2886b967dMD52trueAnonymousREADTEXTAnaPaulaC_Assef_etal_IOC_2019.pdf.txtAnaPaulaC_Assef_etal_IOC_2019.pdf.txtExtracted texttext/plain84599https://arca.fiocruz.br/bitstreams/81360929-36d9-41fc-bd56-7197cdff50ea/downloada052f413992ea2d104c0e4393adf0989MD55falseAnonymousREADTHUMBNAILAnaPaulaC_Assef_etal_IOC_2019.pdf.jpgAnaPaulaC_Assef_etal_IOC_2019.pdf.jpgGenerated Thumbnailimage/jpeg5592https://arca.fiocruz.br/bitstreams/31576b46-3cf9-4142-8a6b-39ba0ce99586/download17ee0ac9fd0b1f77d386aebc535eb1e6MD56falseAnonymousREADicict/338992025-07-29 22:43:35.966open.accessoai:arca.fiocruz.br:icict/33899https://arca.fiocruz.brRepositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352025-07-30T01:43:35Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)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
dc.title.none.fl_str_mv FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
title FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
spellingShingle FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
Merigueti, Thiago Castanheira
Biologia de sistemas
Análise de Balanço de Fluxo
Rede Metabólica
Análise COBRA
Python (linguagem de programação)
Systems biology
Flux balance analysis
Metabolic network
COBRA analysis
Python (programming language)
title_short FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
title_full FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
title_fullStr FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
title_full_unstemmed FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
title_sort FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria
author Merigueti, Thiago Castanheira
author_facet Merigueti, Thiago Castanheira
Carneiro, Marcia Weber
Carvalho-Assef, Ana Paula d' A.
Silva Jr, Floriano Paes
Silva, Fabricio Alves Barbosa da
author_role author
author2 Carneiro, Marcia Weber
Carvalho-Assef, Ana Paula d' A.
Silva Jr, Floriano Paes
Silva, Fabricio Alves Barbosa da
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Merigueti, Thiago Castanheira
Carneiro, Marcia Weber
Carvalho-Assef, Ana Paula d' A.
Silva Jr, Floriano Paes
Silva, Fabricio Alves Barbosa da
dc.subject.other.none.fl_str_mv Biologia de sistemas
Análise de Balanço de Fluxo
Rede Metabólica
Análise COBRA
Python (linguagem de programação)
topic Biologia de sistemas
Análise de Balanço de Fluxo
Rede Metabólica
Análise COBRA
Python (linguagem de programação)
Systems biology
Flux balance analysis
Metabolic network
COBRA analysis
Python (programming language)
dc.subject.en.none.fl_str_mv Systems biology
Flux balance analysis
Metabolic network
COBRA analysis
Python (programming language)
description CAPES, FAPERJ, CNPq e FIOCRUZ (INOVA-FIOCRUZ VPPCB-007-FIO-18-2-29) for financial support.
publishDate 2019
dc.date.accessioned.fl_str_mv 2019-07-09T11:45:07Z
dc.date.available.fl_str_mv 2019-07-09T11:45:07Z
dc.date.issued.fl_str_mv 2019
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.citation.fl_str_mv MERIGUETI, Thiago Castanheira et al. FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. Frontiers in Genetics, v. 10, p. 1-14, July 2019.
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/33899
dc.identifier.issn.none.fl_str_mv 1664-8021
dc.identifier.doi.none.fl_str_mv 10.3389/fgene.2019.00633
identifier_str_mv MERIGUETI, Thiago Castanheira et al. FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. Frontiers in Genetics, v. 10, p. 1-14, July 2019.
1664-8021
10.3389/fgene.2019.00633
url https://arca.fiocruz.br/handle/icict/33899
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://arca.fiocruz.br/bitstreams/8a97e365-9bf1-4ee6-bb7b-603b5aa7e6ba/download
https://arca.fiocruz.br/bitstreams/2b8c1693-fa75-49ea-82f1-f43dc897096a/download
https://arca.fiocruz.br/bitstreams/81360929-36d9-41fc-bd56-7197cdff50ea/download
https://arca.fiocruz.br/bitstreams/31576b46-3cf9-4142-8a6b-39ba0ce99586/download
bitstream.checksum.fl_str_mv 5a560609d32a3863062d77ff32785d58
3f189d37debf3938623bdbf2886b967d
a052f413992ea2d104c0e4393adf0989
17ee0ac9fd0b1f77d386aebc535eb1e6
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
_version_ 1839716149591277568

Similar Items