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

Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; Robert D. Finn; Adrian Fritz; Stephan Fuchs; Georges Hattab; Anne Christin Hauschild; Dominik Heider; Marie Hoffmann; Martin Hölzer; Stefan Hoops; Lars Kaderali; Ioanna Kalvari; Max Von Kleist; Renó Kmiecinski; Denise Kühnert; Gorka Lasso; Pieter Libin; Markus List; Hannah F. Löchel; Maria J. Martin; Roman Martin; Julian Matschinske; Alice C. McHardy; Pedro Mendes; Jaina Mistry; Vincent Navratil; Eric P. Nawrocki; Aíne Niamh O'Toole; Nancy Ontiveros-Palacios; Anton I. Petrov; Guillermo Rangel-Pineros; Nicole Redaschi; Susanne Reimering; Knut Reinert; Alejandro Reyes; Lorna Richardson; David L. Robertson; Sepideh Sadegh; Joshua B. Singer; Kristof Theys; Chris Upton; Marius Welzel; Lowri Williams; Manja Marz

doi:10.1093/bib/bbaa232

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

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin HölzerStefan Hoops, Lars Kaderali, Ioanna Kalvari, Max Von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria J. Martin, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Aíne Niamh O'Toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz

Professur für Data Science in Systems Biology

Publikation: Beitrag in Fachzeitschrift › Übersichtsartikel › Begutachtung

104 Zitate (Scopus)

Abstract

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools 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 get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:[email protected]

Originalsprache	Englisch
Seiten (von - bis)	642-663
Seitenumfang	22
Fachzeitschrift	Briefings in Bioinformatics
Jahrgang	22
Ausgabenummer	2
DOIs	https://doi.org/10.1093/bib/bbaa232
Publikationsstatus	Veröffentlicht - 1 März 2021

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Hufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C., Bateman, A., Baumbach, J., Beerenwinkel, N., Brandt, C., Cacciabue, M., Chuguransky, S., Drechsel, O., Finn, R. D., Fritz, A., Fuchs, S., Hattab, G., Hauschild, A. C., Heider, D., Hoffmann, M., ... Marz, M. (2021). Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22(2), 642-663. https://doi.org/10.1093/bib/bbaa232

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title = "Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and coronavirus research",

abstract = "SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools 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 get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:[email protected]",

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author = "Franziska Hufsky and Kevin Lamkiewicz and Alexandre Almeida and Abdel Aouacheria and Cecilia Arighi and Alex Bateman and Jan Baumbach and Niko Beerenwinkel and Christian Brandt and Marco Cacciabue and Sara Chuguransky and Oliver Drechsel and Finn, {Robert D.} and Adrian Fritz and Stephan Fuchs and Georges Hattab and Hauschild, {Anne Christin} and Dominik Heider and Marie Hoffmann and Martin H{\"o}lzer and Stefan Hoops and Lars Kaderali and Ioanna Kalvari and {Von Kleist}, Max and Ren{\'o} Kmiecinski and Denise K{\"u}hnert and Gorka Lasso and Pieter Libin and Markus List and L{\"o}chel, {Hannah F.} and Martin, {Maria J.} and Roman Martin and Julian Matschinske and McHardy, {Alice C.} and Pedro Mendes and Jaina Mistry and Vincent Navratil and Nawrocki, {Eric P.} and O'Toole, {A{\'i}ne Niamh} and Nancy Ontiveros-Palacios and Petrov, {Anton I.} and Guillermo Rangel-Pineros and Nicole Redaschi and Susanne Reimering and Knut Reinert and Alejandro Reyes and Lorna Richardson and Robertson, {David L.} and Sepideh Sadegh and Singer, {Joshua B.} and Kristof Theys and Chris Upton and Marius Welzel and Lowri Williams and Manja Marz",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s) 2020. Published by Oxford University Press.",

year = "2021",

month = mar,

day = "1",

doi = "10.1093/bib/bbaa232",

language = "English",

volume = "22",

pages = "642--663",

journal = "Briefings in Bioinformatics",

issn = "1467-5463",

publisher = "Oxford University Press",

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Hufsky, F, Lamkiewicz, K, Almeida, A, Aouacheria, A, Arighi, C, Bateman, A, Baumbach, J, Beerenwinkel, N, Brandt, C, Cacciabue, M, Chuguransky, S, Drechsel, O, Finn, RD, Fritz, A, Fuchs, S, Hattab, G, Hauschild, AC, Heider, D, Hoffmann, M, Hölzer, M, Hoops, S, Kaderali, L, Kalvari, I, Von Kleist, M, Kmiecinski, R, Kühnert, D, Lasso, G, Libin, P, List, M, Löchel, HF, Martin, MJ, Martin, R, Matschinske, J, McHardy, AC, Mendes, P, Mistry, J, Navratil, V, Nawrocki, EP, O'Toole, AN, Ontiveros-Palacios, N, Petrov, AI, Rangel-Pineros, G, Redaschi, N, Reimering, S, Reinert, K, Reyes, A, Richardson, L, Robertson, DL, Sadegh, S, Singer, JB, Theys, K, Upton, C, Welzel, M, Williams, L & Marz, M 2021, 'Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and coronavirus research', Briefings in Bioinformatics, Jg. 22, Nr. 2, S. 642-663. https://doi.org/10.1093/bib/bbaa232

TY - JOUR

T1 - Computational strategies to combat COVID-19

T2 - Useful tools to accelerate SARS-CoV-2 and coronavirus research

AU - Hufsky, Franziska

AU - Lamkiewicz, Kevin

AU - Almeida, Alexandre

AU - Aouacheria, Abdel

AU - Arighi, Cecilia

AU - Bateman, Alex

AU - Baumbach, Jan

AU - Beerenwinkel, Niko

AU - Brandt, Christian

AU - Cacciabue, Marco

AU - Chuguransky, Sara

AU - Drechsel, Oliver

AU - Finn, Robert D.

AU - Fritz, Adrian

AU - Fuchs, Stephan

AU - Hattab, Georges

AU - Hauschild, Anne Christin

AU - Heider, Dominik

AU - Hoffmann, Marie

AU - Hölzer, Martin

AU - Hoops, Stefan

AU - Kaderali, Lars

AU - Kalvari, Ioanna

AU - Von Kleist, Max

AU - Kmiecinski, Renó

AU - Kühnert, Denise

AU - Lasso, Gorka

AU - Libin, Pieter

AU - List, Markus

AU - Löchel, Hannah F.

AU - Martin, Maria J.

AU - Martin, Roman

AU - Matschinske, Julian

AU - McHardy, Alice C.

AU - Mendes, Pedro

AU - Mistry, Jaina

AU - Navratil, Vincent

AU - Nawrocki, Eric P.

AU - O'Toole, Aíne Niamh

AU - Ontiveros-Palacios, Nancy

AU - Petrov, Anton I.

AU - Rangel-Pineros, Guillermo

AU - Redaschi, Nicole

AU - Reimering, Susanne

AU - Reinert, Knut

AU - Reyes, Alejandro

AU - Richardson, Lorna

AU - Robertson, David L.

AU - Sadegh, Sepideh

AU - Singer, Joshua B.

AU - Theys, Kristof

AU - Upton, Chris

AU - Welzel, Marius

AU - Williams, Lowri

AU - Marz, Manja

PY - 2021/3/1

Y1 - 2021/3/1

N2 - SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools 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 get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:[email protected]

AB - SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools 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 get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:[email protected]

KW - SARS-CoV-2

KW - drug design

KW - epidemiology

KW - sequencing

KW - tools

KW - virus bioinformatics

UR - http://www.scopus.com/inward/record.url?scp=85103474550&partnerID=8YFLogxK

U2 - 10.1093/bib/bbaa232

DO - 10.1093/bib/bbaa232

M3 - Review article

C2 - 33147627

AN - SCOPUS:85103474550

SN - 1467-5463

VL - 22

SP - 642

EP - 663

JO - Briefings in Bioinformatics

JF - Briefings in Bioinformatics

IS - 2

ER -

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

Abstract

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