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Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; Bateman, Alex; Baumbach, Jan; Beerenwinkel, Niko; Brandt, Christian; Cacciabue, Marco; Chuguransky, Sara; 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; Martin, Maria J; Martin, Roman; Matschinske, Julian; McHardy, Alice C; Mendes, Pedro; Mistry, Jaina; Navratil, Vincent; Nawrocki, Eric P; O'Toole, Áine Niamh; Ontiveros-Palacios, Nancy; Petrov, Anton I; Rangel-Pineros, Guillermo; Redaschi, Nicole; Reimering, Susanne; Reinert, Knut; Reyes, Alejandro; Richardson, Lorna; Robertson, David L; Sadegh, Sepideh; Singer, Joshua B.
  • Hufsky F; Friedrich-Schiller-University Jena, Germany.
  • Lamkiewicz K; Friedrich-Schiller-University Jena, Germany.
  • Almeida A; EMBL-EBI and the Wellcome Sanger Institute, UK.
  • Aouacheria A; CNRS, France.
  • Arighi C; Biocuration and Literature Access at PIR, USA.
  • Bateman A; Protein Sequence Resources at EMBL-EBI, UK.
  • Baumbach J; Technical University of Munich, Germany.
  • Beerenwinkel N; Computational Biology at ETH Zurich, Switzerland.
  • Brandt C; Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany.
  • Cacciabue M; Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina.
  • Chuguransky S; Pfam and InterPro databases, at the EMBL-EBI, UK.
  • Drechsel O; bioinformatics department at the Robert Koch-Institute, Germany.
  • Finn RD; Pfam and MGnify.
  • Fritz A; Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany.
  • Fuchs S; bioinformatics department at the Robert Koch-Institute, Germany.
  • Hattab G; Bioinformatics Division at Philipps-University Marburg, Germany.
  • Hauschild AC; Philipps-University Marburg, Germany.
  • Heider D; Data Science in Biomedicine at the Philipps-University of Marburg, Germany.
  • Hoffmann M; Freie Universität Berlin, Germany.
  • Hölzer M; Friedrich Schiller University Jena, Germany.
  • Hoops S; Biocomplexity Institute and Initiative at the University of Virginia, USA.
  • Kaderali L; Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany.
  • Kalvari I; Senior Software Developer.
  • von Kleist M; bioinformatics department at the Robert Koch-Institute, Germany.
  • Kmiecinski R; bioinformatics department at the Robert Koch-Institute, Germany.
  • Kühnert D; Max Planck Institute for the Science of Human History.
  • Lasso G; Chandran Lab, Albert Einstein College of Medicine, USA.
  • Libin P; University of Hasselt, Belgium.
  • List M; Technical University of Munich, Germany.
  • Löchel HF; Philipps-University Marburg, Germany.
  • Martin MJ; EMBL-EBI, UK.
  • Martin R; Philipps-University Marburg, Germany.
  • Matschinske J; Chair of Experimental Bioinformatics at TU Munich, Germany.
  • McHardy AC; Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany.
  • Mendes P; Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA.
  • Mistry J; EMBL-EBI, UK.
  • Navratil V; Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France.
  • Nawrocki EP; National Center for Biotechnology Information (NCBI).
  • O'Toole ÁN; Rambaut group at Edinburgh University, UK.
  • Ontiveros-Palacios N; EMBL-EBI, UK.
  • Petrov AI; EMBL-EBI, UK.
  • Rangel-Pineros G; GLOBE Institute in the University of Copenhagen, Denmark.
  • Redaschi N; Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone).
  • Reimering S; Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research.
  • Reinert K; Freie Universität Berlin, Germany.
  • Reyes A; Universidad de los Andes, Colombia.
  • Richardson L; Sequence Families team at EMBL-EBI, UK.
  • Robertson DL; MRC-University of Glasgow Centre for Virus Research, UK.
  • Sadegh S; Chair of Experimental Bioinformatics at Technical University of Munich, Germany.
  • Singer JB; MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK.
Brief Bioinform ; 22(2): 642-663, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1343629
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. Contactevbc@unj-jena.de.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Computational Biology / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study Limits: Humans Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article Affiliation country: Bib

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Computational Biology / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study Limits: Humans Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article Affiliation country: Bib