Literature DB >> 34588690

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.

Wolfgang Maier1, Simon Bray1, Marius van den Beek2, Dave Bouvier2, Nathan Coraor2, Milad Miladi1, Babita Singh3, Jordi Rambla De Argila3, Dannon Baker4, Nathan Roach5, Simon Gladman6, Frederik Coppens7,8, Darren P Martin9, Andrew Lonie6, Björn Grüning10, Sergei L Kosakovsky Pond11, Anton Nekrutenko12.   

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Year:  2021        PMID: 34588690      PMCID: PMC8845060          DOI: 10.1038/s41587-021-01069-1

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  10 in total

1.  Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.

Authors:  Darren P Martin; Spyros Lytras; Alexander G Lucaci; Wolfgang Maier; Björn Grüning; Stephen D Shank; Steven Weaver; Oscar A MacLean; Richard J Orton; Philippe Lemey; Maciej F Boni; Houriiyah Tegally; Gordon Harkins; Cathrine Scheepers; Jinal N Bhiman; Josie Everatt; Daniel G Amoako; James Emmanuel San; Jennifer Giandhari; Alex Sigal; Carolyn Williamson; Nei-Yuan Hsiao; Anne von Gottberg; Arne De Klerk; Robert W Shafer; David L Robertson; Robert J Wilkinson; B Trevor Sewell; Richard Lessells; Anton Nekrutenko; Allison J Greaney; Tyler N Starr; Jesse D Bloom; Ben Murrell; Eduan Wilkinson; Ravindra K Gupta; Tulio de Oliveira; Sergei L Kosakovsky Pond
Journal:  bioRxiv       Date:  2022-01-18

2.  Genomic evidence for divergent co-infections of co-circulating SARS-CoV-2 lineages.

Authors:  Hang-Yu Zhou; Ye-Xiao Cheng; Lin Xu; Jia-Ying Li; Chen-Yue Tao; Cheng-Yang Ji; Na Han; Rong Yang; Hui Wu; Yaling Li; Aiping Wu
Journal:  Comput Struct Biotechnol J       Date:  2022-07-28       Impact factor: 6.155

3.  Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.

Authors:  Joel O Wertheim; Jade C Wang; Mindy Leelawong; Darren P Martin; Jennifer L Havens; Moinuddin A Chowdhury; Jonathan E Pekar; Helly Amin; Anthony Arroyo; Gordon A Awandare; Hoi Yan Chow; Edimarlyn Gonzalez; Elizabeth Luoma; Collins M Morang'a; Anton Nekrutenko; Stephen D Shank; Stefan Silver; Peter K Quashie; Jennifer L Rakeman; Victoria Ruiz; Lucia V Torian; Tetyana I Vasylyeva; Sergei L Kosakovsky Pond; Scott Hughes
Journal:  Nat Commun       Date:  2022-06-25       Impact factor: 17.694

4.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.

Authors: 
Journal:  Nucleic Acids Res       Date:  2022-04-21       Impact factor: 19.160

5.  External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.

Authors:  Fanny Wegner; Tim Roloff; Gilbert Greub; Adrian Egli; Michael Huber; Samuel Cordey; Alban Ramette; Yannick Gerth; Claire Bertelli; Madlen Stange; Helena M B Seth-Smith; Alfredo Mari; Karoline Leuzinger; Lorenzo Cerutti; Keith Harshman; Ioannis Xenarios; Philippe Le Mercier; Pascal Bittel; Stefan Neuenschwander; Onya Opota; Jonas Fuchs; Marcus Panning; Charlotte Michel; Marie Hallin; Thomas Demuyser; Ricardo De Mendonca; Paul Savelkoul; Jozef Dingemans; Brian van der Veer; Stefan A Boers; Eric C J Claas; Jordy P M Coolen; Willem J G Melchers; Marianne Gunell; Teemu Kallonen; Tytti Vuorinen; Antti J Hakanen; Eva Bernhoff; Marit Andrea Klokkhammer Hetland; Hadar Golan Berman; Sheera Adar; Jacob Moran-Gilad; Dana G Wolf; Stephen L Leib; Oliver Nolte; Laurent Kaiser; Stefan Schmutz; Verena Kufner; Maryam Zaheri; Alexandra Trkola; Hege Vangstein Aamot; Hans H Hirsch
Journal:  J Clin Microbiol       Date:  2021-11-10       Impact factor: 5.948

6.  Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines.

Authors:  Connor G G Bamford; Lindsay Broadbent; Elihu Aranday-Cortes; Mary McCabe; James McKenna; David G Courtney; Olivier Touzelet; Ahlam Ali; Grace Roberts; Guillermo Lopez Campos; David Simpson; Conall McCaughey; Derek Fairley; Ken Mills; Ultan F Power
Journal:  Viruses       Date:  2022-02-05       Impact factor: 5.818

7.  EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

Authors:  Chien-Chi Lo; Migun Shakya; Ryan Connor; Karen Davenport; Mark Flynn; Adán Myers Y Gutiérrez; Bin Hu; Po-E Li; Elais Player Jackson; Yan Xu; Patrick S G Chain
Journal:  Bioinformatics       Date:  2022-05-13       Impact factor: 6.937

8.  Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics.

Authors:  Chamteut Oh; Palash Sashittal; Aijia Zhou; Leyi Wang; Mohammed El-Kebir; Thanh H Nguyen
Journal:  Appl Environ Microbiol       Date:  2022-03-14       Impact factor: 4.792

9.  VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis.

Authors:  Pietro Pinoli; Anna Bernasconi; Anna Sandionigi; Stefano Ceri
Journal:  BioTech (Basel)       Date:  2021-11-06

10.  Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.

Authors:  Darren P Martin; Spyros Lytras; Alexander G Lucaci; Wolfgang Maier; Björn Grüning; Stephen D Shank; Steven Weaver; Oscar A MacLean; Richard J Orton; Philippe Lemey; Maciej F Boni; Houriiyah Tegally; Gordon W Harkins; Cathrine Scheepers; Jinal N Bhiman; Josie Everatt; Daniel G Amoako; James Emmanuel San; Jennifer Giandhari; Alex Sigal; Carolyn Williamson; Nei-Yuan Hsiao; Anne von Gottberg; Arne De Klerk; Robert W Shafer; David L Robertson; Robert J Wilkinson; B Trevor Sewell; Richard Lessells; Anton Nekrutenko; Allison J Greaney; Tyler N Starr; Jesse D Bloom; Ben Murrell; Eduan Wilkinson; Ravindra K Gupta; Tulio de Oliveira; Sergei L Kosakovsky Pond
Journal:  Mol Biol Evol       Date:  2022-04-11       Impact factor: 8.800

  10 in total

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