Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Autores: Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; Bateman, Alex; Baumbach, Jan; Beerenwinkel, Niko; Brandt, Christian; Cacciabue, Marco Polo Domingo; Chuguransky, Sara Rocío; Drechsel, Oliver; Finn, Robert D.; Fritz, Adrian; Fuchs, Stephan; Hattab, Georges; Hauschild, Anne Christin; Heider, Dominik; Hoffmann, Marie; Hölzer, Martin; Hoops, Stefan; Kaderali, Lars; Kalvari, Ioanna; von Kleist, Max; Kmiecinski, Renó; Kühnert, Denise; Lasso, Gorka; Libin, Pieter; List, Markus; Löchel, Hannah F.
Año de publicación: 2020
Idioma: inglés
Tipo de recurso: artículo
Estado: versión publicada
Descripción: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causesthe infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformaticstools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection,understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to getinsight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for theroutine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemicand evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets anddevelopment of therapeutic strategies. For each tool, we briefly describe its use case and how it advances researchspecifically for SARS-CoV-2.
Fil: Hufsky, Franziska. Friedrich Schiller University Jena; Alemania
Fil: Lamkiewicz, Kevin. Friedrich Schiller University Jena; Alemania
Fil: Almeida, Alexandre. the Wellcome Sanger Institute; Reino Unido
Fil: Aouacheria, Abdel. Centre National de la Recherche Scientifique; Francia
Fil: Arighi, Cecilia. Biocuration and Literature Access at PIR; Estados Unidos
Fil: Bateman, Alex. European Bioinformatics Institute. Head of Protein Sequence Resources; Reino Unido
Fil: Baumbach, Jan. Universitat Technical Zu Munich; Alemania
Fil: Beerenwinkel, Niko. Universitat Technical Zu Munich; Alemania
Fil: Brandt, Christian. Jena University Hospital; Alemania
Fil: Cacciabue, Marco Polo Domingo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Chuguransky, Sara Rocío. European Bioinformatics Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Drechsel, Oliver. Robert Koch-Institute; Alemania
Fil: Finn, Robert D.. Biocurator for Pfam and InterPro databases; Reino Unido
Fil: Fritz, Adrian. Helmholtz Centre for Infection Research; Alemania
Fil: Fuchs, Stephan. Robert Koch-Institute; Alemania
Fil: Hattab, Georges. University Marburg; Alemania
Fil: Hauschild, Anne Christin. University Marburg; Alemania
Fil: Heider, Dominik. University Marburg; Alemania
Fil: Hoffmann, Marie. Freie Universität Berlin; Alemania
Fil: Hölzer, Martin. Friedrich Schiller University Jena; Alemania
Fil: Hoops, Stefan. University of Virginia; Estados Unidos
Fil: Kaderali, Lars. University Medicine Greifswald; Alemania
Fil: Kalvari, Ioanna. European Bioinformatics Institute; Reino Unido
Fil: von Kleist, Max. Robert Koch-Institute; Alemania
Fil: Kmiecinski, Renó. Robert Koch-Institute; Alemania
Fil: Kühnert, Denise. Max Planck Institute for the Science of Human History; Alemania
Fil: Lasso, Gorka. Albert Einstein College of Medicine; Estados Unidos
Fil: Libin, Pieter. Hasselt University; Bélgica
Fil: List, Markus. Universitat Technical Zu Munich; Alemania
Fil: Löchel, Hannah F.. University Marburg; Alemania
Materia: VIRUS BIOINFORMATICS
SARS-COV-2
EPIDEMIOLOGY
TOOLS
COVID-19
Nivel de accesibilidad: acceso abierto
Condiciones de uso: https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
Institución: Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador: oai:ri.conicet.gov.ar:11336/128424

Acceder

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network_name_str	CONICET Digital (CONICET)
spelling	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus researchHufsky, FranziskaLamkiewicz, KevinAlmeida, AlexandreAouacheria, AbdelArighi, CeciliaBateman, AlexBaumbach, JanBeerenwinkel, NikoBrandt, ChristianCacciabue, Marco Polo DomingoChuguransky, Sara RocíoDrechsel, OliverFinn, Robert D.Fritz, AdrianFuchs, StephanHattab, GeorgesHauschild, Anne ChristinHeider, DominikHoffmann, MarieHölzer, MartinHoops, StefanKaderali, LarsKalvari, Ioannavon Kleist, MaxKmiecinski, RenóKühnert, DeniseLasso, GorkaLibin, PieterList, MarkusLöchel, Hannah F.VIRUS BIOINFORMATICSSARS-COV-2EPIDEMIOLOGYTOOLSCOVID-19https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causesthe infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformaticstools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection,understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to getinsight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for theroutine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemicand evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets anddevelopment of therapeutic strategies. For each tool, we briefly describe its use case and how it advances researchspecifically for SARS-CoV-2.Fil: Hufsky, Franziska. Friedrich Schiller University Jena; AlemaniaFil: Lamkiewicz, Kevin. Friedrich Schiller University Jena; AlemaniaFil: Almeida, Alexandre. the Wellcome Sanger Institute; Reino UnidoFil: Aouacheria, Abdel. Centre National de la Recherche Scientifique; FranciaFil: Arighi, Cecilia. Biocuration and Literature Access at PIR; Estados UnidosFil: Bateman, Alex. European Bioinformatics Institute. Head of Protein Sequence Resources; Reino UnidoFil: Baumbach, Jan. Universitat Technical Zu Munich; AlemaniaFil: Beerenwinkel, Niko. Universitat Technical Zu Munich; AlemaniaFil: Brandt, Christian. Jena University Hospital; AlemaniaFil: Cacciabue, Marco Polo Domingo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Chuguransky, Sara Rocío. European Bioinformatics Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Drechsel, Oliver. Robert Koch-Institute; AlemaniaFil: Finn, Robert D.. Biocurator for Pfam and InterPro databases; Reino UnidoFil: Fritz, Adrian. Helmholtz Centre for Infection Research; AlemaniaFil: Fuchs, Stephan. Robert Koch-Institute; AlemaniaFil: Hattab, Georges. University Marburg; AlemaniaFil: Hauschild, Anne Christin. University Marburg; AlemaniaFil: Heider, Dominik. University Marburg; AlemaniaFil: Hoffmann, Marie. Freie Universität Berlin; AlemaniaFil: Hölzer, Martin. Friedrich Schiller University Jena; AlemaniaFil: Hoops, Stefan. University of Virginia; Estados UnidosFil: Kaderali, Lars. University Medicine Greifswald; AlemaniaFil: Kalvari, Ioanna. European Bioinformatics Institute; Reino UnidoFil: von Kleist, Max. Robert Koch-Institute; AlemaniaFil: Kmiecinski, Renó. Robert Koch-Institute; AlemaniaFil: Kühnert, Denise. Max Planck Institute for the Science of Human History; AlemaniaFil: Lasso, Gorka. Albert Einstein College of Medicine; Estados UnidosFil: Libin, Pieter. Hasselt University; BélgicaFil: List, Markus. Universitat Technical Zu Munich; AlemaniaFil: Löchel, Hannah F.. University Marburg; AlemaniaOxford University Press2020-11-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/128424Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; et al.; Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research; Oxford University Press; Briefings In Bioinformatics; bbaa232; 4-11-2020; 1-221467-5463CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa232/5955939info:eu-repo/semantics/altIdentifier/doi/10.1093/bib/bbaa232info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:38:16Zoai:ri.conicet.gov.ar:11336/128424instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:38:17.145CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
title	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
spellingShingle	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research Hufsky, Franziska VIRUS BIOINFORMATICS SARS-COV-2 EPIDEMIOLOGY TOOLS COVID-19
title_short	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
title_full	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
title_fullStr	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
title_full_unstemmed	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
title_sort	Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
dc.creator.none.fl_str_mv	Hufsky, Franziska Lamkiewicz, Kevin Almeida, Alexandre Aouacheria, Abdel Arighi, Cecilia Bateman, Alex Baumbach, Jan Beerenwinkel, Niko Brandt, Christian Cacciabue, Marco Polo Domingo Chuguransky, Sara Rocío Drechsel, Oliver Finn, Robert D. Fritz, Adrian Fuchs, Stephan Hattab, Georges Hauschild, Anne Christin Heider, Dominik Hoffmann, Marie Hölzer, Martin Hoops, Stefan Kaderali, Lars Kalvari, Ioanna von Kleist, Max Kmiecinski, Renó Kühnert, Denise Lasso, Gorka Libin, Pieter List, Markus Löchel, Hannah F.
author	Hufsky, Franziska
author_facet	Hufsky, Franziska Lamkiewicz, Kevin Almeida, Alexandre Aouacheria, Abdel Arighi, Cecilia Bateman, Alex Baumbach, Jan Beerenwinkel, Niko Brandt, Christian Cacciabue, Marco Polo Domingo Chuguransky, Sara Rocío Drechsel, Oliver Finn, Robert D. Fritz, Adrian Fuchs, Stephan Hattab, Georges Hauschild, Anne Christin Heider, Dominik Hoffmann, Marie Hölzer, Martin Hoops, Stefan Kaderali, Lars Kalvari, Ioanna von Kleist, Max Kmiecinski, Renó Kühnert, Denise Lasso, Gorka Libin, Pieter List, Markus Löchel, Hannah F.
author_role	author
author2	Lamkiewicz, Kevin Almeida, Alexandre Aouacheria, Abdel Arighi, Cecilia Bateman, Alex Baumbach, Jan Beerenwinkel, Niko Brandt, Christian Cacciabue, Marco Polo Domingo Chuguransky, Sara Rocío Drechsel, Oliver Finn, Robert D. Fritz, Adrian Fuchs, Stephan Hattab, Georges Hauschild, Anne Christin Heider, Dominik Hoffmann, Marie Hölzer, Martin Hoops, Stefan Kaderali, Lars Kalvari, Ioanna von Kleist, Max Kmiecinski, Renó Kühnert, Denise Lasso, Gorka Libin, Pieter List, Markus Löchel, Hannah F.
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
dc.subject.none.fl_str_mv	VIRUS BIOINFORMATICS SARS-COV-2 EPIDEMIOLOGY TOOLS COVID-19
topic	VIRUS BIOINFORMATICS SARS-COV-2 EPIDEMIOLOGY TOOLS COVID-19
purl_subject.fl_str_mv	https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv	SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causesthe infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformaticstools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection,understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to getinsight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for theroutine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemicand evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets anddevelopment of therapeutic strategies. For each tool, we briefly describe its use case and how it advances researchspecifically for SARS-CoV-2. Fil: Hufsky, Franziska. Friedrich Schiller University Jena; Alemania Fil: Lamkiewicz, Kevin. Friedrich Schiller University Jena; Alemania Fil: Almeida, Alexandre. the Wellcome Sanger Institute; Reino Unido Fil: Aouacheria, Abdel. Centre National de la Recherche Scientifique; Francia Fil: Arighi, Cecilia. Biocuration and Literature Access at PIR; Estados Unidos Fil: Bateman, Alex. European Bioinformatics Institute. Head of Protein Sequence Resources; Reino Unido Fil: Baumbach, Jan. Universitat Technical Zu Munich; Alemania Fil: Beerenwinkel, Niko. Universitat Technical Zu Munich; Alemania Fil: Brandt, Christian. Jena University Hospital; Alemania Fil: Cacciabue, Marco Polo Domingo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Chuguransky, Sara Rocío. European Bioinformatics Institute; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Drechsel, Oliver. Robert Koch-Institute; Alemania Fil: Finn, Robert D.. Biocurator for Pfam and InterPro databases; Reino Unido Fil: Fritz, Adrian. Helmholtz Centre for Infection Research; Alemania Fil: Fuchs, Stephan. Robert Koch-Institute; Alemania Fil: Hattab, Georges. University Marburg; Alemania Fil: Hauschild, Anne Christin. University Marburg; Alemania Fil: Heider, Dominik. University Marburg; Alemania Fil: Hoffmann, Marie. Freie Universität Berlin; Alemania Fil: Hölzer, Martin. Friedrich Schiller University Jena; Alemania Fil: Hoops, Stefan. University of Virginia; Estados Unidos Fil: Kaderali, Lars. University Medicine Greifswald; Alemania Fil: Kalvari, Ioanna. European Bioinformatics Institute; Reino Unido Fil: von Kleist, Max. Robert Koch-Institute; Alemania Fil: Kmiecinski, Renó. Robert Koch-Institute; Alemania Fil: Kühnert, Denise. Max Planck Institute for the Science of Human History; Alemania Fil: Lasso, Gorka. Albert Einstein College of Medicine; Estados Unidos Fil: Libin, Pieter. Hasselt University; Bélgica Fil: List, Markus. Universitat Technical Zu Munich; Alemania Fil: Löchel, Hannah F.. University Marburg; Alemania
description	SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causesthe infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformaticstools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection,understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to getinsight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for theroutine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemicand evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets anddevelopment of therapeutic strategies. For each tool, we briefly describe its use case and how it advances researchspecifically for SARS-CoV-2.
publishDate	2020
dc.date.none.fl_str_mv	2020-11-04
dc.type.none.fl_str_mv	info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo
format	article
status_str	publishedVersion
dc.identifier.none.fl_str_mv	http://hdl.handle.net/11336/128424 Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; et al.; Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research; Oxford University Press; Briefings In Bioinformatics; bbaa232; 4-11-2020; 1-22 1467-5463 CONICET Digital CONICET
url	http://hdl.handle.net/11336/128424
identifier_str_mv	Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; et al.; Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research; Oxford University Press; Briefings In Bioinformatics; bbaa232; 4-11-2020; 1-22 1467-5463 CONICET Digital CONICET
dc.language.none.fl_str_mv	eng
language	eng
dc.relation.none.fl_str_mv	info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa232/5955939 info:eu-repo/semantics/altIdentifier/doi/10.1093/bib/bbaa232
dc.rights.none.fl_str_mv	info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv	openAccess
rights_invalid_str_mv	https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv	application/pdf 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:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str	CONICET Digital (CONICET)
collection	CONICET Digital (CONICET)
instname_str	Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv	CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv	dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score	13.070432

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

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