publication . Other literature type . Article . Preprint . 2020 . Embargo end date: 09 Aug 2021

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 N. Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; ...
Open Access
  • Published: 04 Nov 2020
  • Publisher: Freie Universität Berlin
Abstract
ISSN:1477-4054
Subjects
Medical Subject Headings: virusesvirus diseases
free text keywords: virus bioinformatics, SARS-CoV-2, sequencing, epidemiology, drug design, tools, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie, VIRUS BIOINFORMATICS, SARS-COV-2, EPIDEMIOLOGY, TOOLS, COVID-19, Virología, Ciencias Biológicas, CIENCIAS NATURALES Y EXACTAS, Otras Ciencias de la Computación e Información, Ciencias de la Computación e Información, [SDV.IMM.IMM]Life Sciences [q-bio]/Immunology/Immunotherapy, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [INFO.INFO-BT]Computer Science [cs]/Biotechnology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], virus bioinformatics; Sars-Cov-2; sequencing; epidemiology; drug design; tools, Science & Technology, Life Sciences & Biomedicine, Biochemical Research Methods, Mathematical & Computational Biology, Biochemistry & Molecular Biology, sequencing, drug design, PHYLOGENETIC ANALYSIS, PROTEIN INTERACTIONS, FUNCTIONAL RECEPTOR, GENOME, DATABASE, RNA, RESOURCE, VISUALIZATION, REPLICATION, ANNOTATION, virology, Method Review, AcademicSubjects/SCI01060, Molecular Biology, Information Systems, 610 Medizin und Gesundheit, ddc:570, ddc:500, ddc:610, Coronavirus disease 2019 (COVID-19), Medicine, business.industry, business, Virology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronavirus, medicine.disease_cause, Family Coronaviridae, Novel virus, Bioinformatics workflows, Pandemic, Infectious disease (medical specialty), Computational biology
Communities
Communities with gateway
OpenAIRE Connect image
Funded by
UKRI| Capacity building for bioinformatics in Latin America
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: BB/P027849/1
  • Funding stream: BBSRC
,
NIH| UniProt supporting an integrated multidisciplinary research agenda for Alzheimer's Disease
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24HG007822-05S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
UKRI| Bilateral NSF/BIO-BBSRC:A Metagenomics Exchange - enriching analysis by synergistic harmonisation of MG-RAST and the EBI Metagenomics Portal
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: BB/N018354/1
  • Funding stream: BBSRC
,
EC| REPO-TRIAL
Project
REPO-TRIAL
An in silico-based approach to improve the efficacy and precision of drug REPurpOsing TRIALs for a mechanism-based patient cohort with predominant cerebro-cardiovascular phenotypes
  • Funder: European Commission (EC)
  • Project Code: 777111
  • Funding stream: H2020 | RIA
Validated by funder
,
WT| University of Edinburgh - Hosts, Pathogens & Global Health
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 203783
  • Funding stream: Pathogen Biology and Disease Transmission
125 references, page 1 of 9

1. Aguilera LU, Rodríguez-González J. Modeling the effect of tat inhibitors on HIV latency. J Theor Biol 2019;473:20-7.

2. Akgül A, Khoshnaw SHA, Mohammed WH. Mathematical model for the ebola virus disease. J Adv Phys 2018;7(2):190-8.

3. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res 2000;28(1):304-5.

4. J. K. Barry. Mathematical modelling of the HIV life cycle: identifying optimal treatment strategies. PhD thesis, University of Greifswald, 2018.

5. C. Boettiger. An introduction to docker for reproducible research. ACM SIGOPS Operating Systems Review, 2015; 49(1):71-79. [OpenAIRE]

6. Bouckaert R, Vaughan TG, Barido-Sottani J, et al. BEAST 2.5: An advanced software platform for bayesian evolutionary analysis. PLoS Comput Biol 2019;15(4):e1006650.

7. Breiman L. Random forests. Mach Learn 2001;45(1):5-32.

8. Brockmann D, Helbing D. The hidden geometry of complex, network-driven contagion phenomena. Science 2013;342(6164):1337-42.

9. Brodie R, Smith AJ, Roper RL, et al. Base-by-base: Single nucleotide-level analysis of whole viral genome alignments. BMC Bioinformatics 2004;5(1):96.

10. W. Chang, J. Cheng, J. Allaire, Y. Xie, and J. Mcpherson. shiny: Web application framework for r. r package version 1.4.0.2., 2020.

11. Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 2020;25(3).

12. Cuypers L, Li G, Neumann-Haefelin C, et al. Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development. Virus Evol 2016;2(2):vew024.

13. Cuypers L, Libin P, Schrooten Y, et al. Exploring resistance pathways for first-generation NS3/4A protease inhibitors boceprevir and telaprevir using Bayesian network learning. Infect Genet Evol 2017;53:15-23.

14. De Maio N, Worby CJ, Wilson DJ, et al. Bayesian reconstruction of transmission within outbreaks using genomic variants. PLoS Comput Biol 2018;14(4):e1006117.

15. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011;7(10):e1002195.

125 references, page 1 of 9
Abstract
ISSN:1477-4054
Subjects
Medical Subject Headings: virusesvirus diseases
free text keywords: virus bioinformatics, SARS-CoV-2, sequencing, epidemiology, drug design, tools, 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie, VIRUS BIOINFORMATICS, SARS-COV-2, EPIDEMIOLOGY, TOOLS, COVID-19, Virología, Ciencias Biológicas, CIENCIAS NATURALES Y EXACTAS, Otras Ciencias de la Computación e Información, Ciencias de la Computación e Información, [SDV.IMM.IMM]Life Sciences [q-bio]/Immunology/Immunotherapy, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [INFO.INFO-BT]Computer Science [cs]/Biotechnology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], virus bioinformatics; Sars-Cov-2; sequencing; epidemiology; drug design; tools, Science & Technology, Life Sciences & Biomedicine, Biochemical Research Methods, Mathematical & Computational Biology, Biochemistry & Molecular Biology, sequencing, drug design, PHYLOGENETIC ANALYSIS, PROTEIN INTERACTIONS, FUNCTIONAL RECEPTOR, GENOME, DATABASE, RNA, RESOURCE, VISUALIZATION, REPLICATION, ANNOTATION, virology, Method Review, AcademicSubjects/SCI01060, Molecular Biology, Information Systems, 610 Medizin und Gesundheit, ddc:570, ddc:500, ddc:610, Coronavirus disease 2019 (COVID-19), Medicine, business.industry, business, Virology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Coronavirus, medicine.disease_cause, Family Coronaviridae, Novel virus, Bioinformatics workflows, Pandemic, Infectious disease (medical specialty), Computational biology
Communities
Communities with gateway
OpenAIRE Connect image
Funded by
UKRI| Capacity building for bioinformatics in Latin America
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: BB/P027849/1
  • Funding stream: BBSRC
,
NIH| UniProt supporting an integrated multidisciplinary research agenda for Alzheimer's Disease
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24HG007822-05S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
UKRI| Bilateral NSF/BIO-BBSRC:A Metagenomics Exchange - enriching analysis by synergistic harmonisation of MG-RAST and the EBI Metagenomics Portal
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: BB/N018354/1
  • Funding stream: BBSRC
,
EC| REPO-TRIAL
Project
REPO-TRIAL
An in silico-based approach to improve the efficacy and precision of drug REPurpOsing TRIALs for a mechanism-based patient cohort with predominant cerebro-cardiovascular phenotypes
  • Funder: European Commission (EC)
  • Project Code: 777111
  • Funding stream: H2020 | RIA
Validated by funder
,
WT| University of Edinburgh - Hosts, Pathogens & Global Health
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 203783
  • Funding stream: Pathogen Biology and Disease Transmission
125 references, page 1 of 9

1. Aguilera LU, Rodríguez-González J. Modeling the effect of tat inhibitors on HIV latency. J Theor Biol 2019;473:20-7.

2. Akgül A, Khoshnaw SHA, Mohammed WH. Mathematical model for the ebola virus disease. J Adv Phys 2018;7(2):190-8.

3. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res 2000;28(1):304-5.

4. J. K. Barry. Mathematical modelling of the HIV life cycle: identifying optimal treatment strategies. PhD thesis, University of Greifswald, 2018.

5. C. Boettiger. An introduction to docker for reproducible research. ACM SIGOPS Operating Systems Review, 2015; 49(1):71-79. [OpenAIRE]

6. Bouckaert R, Vaughan TG, Barido-Sottani J, et al. BEAST 2.5: An advanced software platform for bayesian evolutionary analysis. PLoS Comput Biol 2019;15(4):e1006650.

7. Breiman L. Random forests. Mach Learn 2001;45(1):5-32.

8. Brockmann D, Helbing D. The hidden geometry of complex, network-driven contagion phenomena. Science 2013;342(6164):1337-42.

9. Brodie R, Smith AJ, Roper RL, et al. Base-by-base: Single nucleotide-level analysis of whole viral genome alignments. BMC Bioinformatics 2004;5(1):96.

10. W. Chang, J. Cheng, J. Allaire, Y. Xie, and J. Mcpherson. shiny: Web application framework for r. r package version 1.4.0.2., 2020.

11. Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 2020;25(3).

12. Cuypers L, Li G, Neumann-Haefelin C, et al. Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development. Virus Evol 2016;2(2):vew024.

13. Cuypers L, Libin P, Schrooten Y, et al. Exploring resistance pathways for first-generation NS3/4A protease inhibitors boceprevir and telaprevir using Bayesian network learning. Infect Genet Evol 2017;53:15-23.

14. De Maio N, Worby CJ, Wilson DJ, et al. Bayesian reconstruction of transmission within outbreaks using genomic variants. PLoS Comput Biol 2018;14(4):e1006117.

15. Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011;7(10):e1002195.

125 references, page 1 of 9
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