Literature DB >> 33649511

Want to track pandemic variants faster? Fix the bioinformatics bottleneck.

Emma B Hodcroft, Nicola De Maio, Rob Lanfear, Duncan R MacCannell, Bui Quang Minh, Heiko A Schmidt, Alexandros Stamatakis, Nick Goldman, Christophe Dessimoz.   

Abstract

Keywords:  Bioinformatics; Genomics; Public health; SARS-CoV-2

Mesh：

Substances：

Year:  2021        PMID： 33649511     DOI： 10.1038/d41586-021-00525-x

Source DB:  PubMed          Journal:  Nature        ISSN： 0028-0836            Impact factor:   49.962


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  10 in total

1.  Data sharing: Make outbreak research open access.

Authors:  Nathan L Yozwiak; Stephen F Schaffner; Pardis C Sabeti
Journal:  Nature       Date:  2015-02-26       Impact factor: 49.962

2.  Scientists call for fully open sharing of coronavirus genome data.

Authors:  Richard Van Noorden
Journal:  Nature       Date:  2021-02       Impact factor: 49.962

3.  Stability of SARS-CoV-2 phylogenies.

Authors:  Yatish Turakhia; Nicola De Maio; Bryan Thornlow; Landen Gozashti; Robert Lanfear; Conor R Walker; Angie S Hinrichs; Jason D Fernandes; Rui Borges; Greg Slodkowicz; Lukas Weilguny; David Haussler; Nick Goldman; Russell Corbett-Detig
Journal:  PLoS Genet       Date:  2020-11-18       Impact factor: 5.917

4.  Nextstrain: real-time tracking of pathogen evolution.

Authors:  James Hadfield; Colin Megill; Sidney M Bell; John Huddleston; Barney Potter; Charlton Callender; Pavel Sagulenko; Trevor Bedford; Richard A Neher
Journal:  Bioinformatics       Date:  2018-12-01       Impact factor: 6.931

5.  No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2.

Authors:  Lucy van Dorp; Damien Richard; Cedric C S Tan; Liam P Shaw; Mislav Acman; François Balloux
Journal:  Nat Commun       Date:  2020-11-25       Impact factor: 14.919

6.  Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.

Authors:  Tyler N Starr; Allison J Greaney; Sarah K Hilton; Daniel Ellis; Katharine H D Crawford; Adam S Dingens; Mary Jane Navarro; John E Bowen; M Alejandra Tortorici; Alexandra C Walls; Neil P King; David Veesler; Jesse D Bloom
Journal:  Cell       Date:  2020-08-11       Impact factor: 41.582

7.  Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Authors:  Louis du Plessis; John T McCrone; Alexander E Zarebski; Verity Hill; Christopher Ruis; Moritz U G Kraemer; Andrew Rambaut; Oliver G Pybus; Bernardo Gutierrez; Jayna Raghwani; Jordan Ashworth; Rachel Colquhoun; Thomas R Connor; Nuno R Faria; Ben Jackson; Nicholas J Loman; Áine O'Toole; Samuel M Nicholls; Kris V Parag; Emily Scher; Tetyana I Vasylyeva; Erik M Volz; Alexander Watts; Isaac I Bogoch; Kamran Khan; David M Aanensen
Journal:  Science       Date:  2021-01-08       Impact factor: 47.728

8.  Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.

Authors:  Jacob E Lemieux; Katherine J Siddle; Glen R Gallagher; Lawrence C Madoff; Sandra Smole; Virginia M Pierce; Eric Rosenberg; Pardis C Sabeti; Daniel J Park; Bronwyn L MacInnis; Bennett M Shaw; Christine Loreth; Stephen F Schaffner; Adrianne Gladden-Young; Gordon Adams; Timelia Fink; Christopher H Tomkins-Tinch; Lydia A Krasilnikova; Katherine C DeRuff; Melissa Rudy; Matthew R Bauer; Kim A Lagerborg; Erica Normandin; Sinéad B Chapman; Steven K Reilly; Melis N Anahtar; Aaron E Lin; Amber Carter; Cameron Myhrvold; Molly E Kemball; Sushma Chaluvadi; Caroline Cusick; Katelyn Flowers; Anna Neumann; Felecia Cerrato; Maha Farhat; Damien Slater; Jason B Harris; John A Branda; David Hooper; Jessie M Gaeta; Travis P Baggett; James O'Connell; Andreas Gnirke; Tami D Lieberman; Anthony Philippakis; Meagan Burns; Catherine M Brown; Jeremy Luban; Edward T Ryan; Sarah E Turbett; Regina C LaRocque; William P Hanage
Journal:  Science       Date:  2020-12-10       Impact factor: 47.728

9.  Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.

Authors:  Jemma L Geoghegan; Xiaoyun Ren; Matthew Storey; James Hadfield; Lauren Jelley; Sarah Jefferies; Jill Sherwood; Shevaun Paine; Sue Huang; Jordan Douglas; Fábio K Mendes; Andrew Sporle; Michael G Baker; David R Murdoch; Nigel French; Colin R Simpson; David Welch; Alexei J Drummond; Edward C Holmes; Sebastián Duchêne; Joep de Ligt
Journal:  Nat Commun       Date:  2020-12-11       Impact factor: 14.919

Review 10.  Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing.

Authors:  Tara Swadi; Jemma L Geoghegan; Tom Devine; Caroline McElnay; Jillian Sherwood; Phil Shoemack; Xiaoyun Ren; Matt Storey; Sarah Jefferies; Erasmus Smit; James Hadfield; Aoife Kenny; Lauren Jelley; Andrew Sporle; Andrea McNeill; G Edwin Reynolds; Kip Mouldey; Lindsay Lowe; Gerard Sonder; Alexei J Drummond; Sue Huang; David Welch; Edward C Holmes; Nigel French; Colin R Simpson; Joep de Ligt
Journal:  Emerg Infect Dis       Date:  2021-01-05       Impact factor: 16.126
  10 in total
  24 in total

1.  poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

Authors:  Christian Brandt; Sebastian Krautwurst; Riccardo Spott; Mara Lohde; Mateusz Jundzill; Mike Marquet; Martin Hölzer
Journal:  Front Genet       Date:  2021-07-28       Impact factor: 4.599

2.  Identifying SARS-CoV-2 regional introductions and transmission clusters in real time.

Authors:  Jakob McBroome; Jennifer Martin; Adriano de Bernardi Schneider; Yatish Turakhia; Russell Corbett-Detig
Journal:  Virus Evol       Date:  2022-06-16

3.  VGsim: Scalable viral genealogy simulator for global pandemic.

Authors:  Vladimir Shchur; Vadim Spirin; Dmitry Sirotkin; Evgeni Burovski; Nicola De Maio; Russell Corbett-Detig
Journal:  PLoS Comput Biol       Date:  2022-08-24       Impact factor: 4.779

4.  Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.

Authors:  Laura Hughes; Karthik Gangavarapu; Alaa Abdel Latif; Julia Mullen; Manar Alkuzweny; Emory Hufbauer; Ginger Tsueng; Emily Haag; Mark Zeller; Christine Aceves; Karina Zaiets; Marco Cano; Jerry Zhou; Zhongchao Qian; Rachel Sattler; Nathaniel Matteson; Joshua Levy; Raphael Lee; Lucas Freitas; Sebastian Maurer-Stroh; Marc Suchard; Chunlei Wu; Andrew Su; Kristian Andersen
Journal:  Res Sq       Date:  2022-06-28

Review 5.  Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.

Authors:  Stephen W Attwood; Sarah C Hill; David M Aanensen; Thomas R Connor; Oliver G Pybus
Journal:  Nat Rev Genet       Date:  2022-04-22       Impact factor: 59.581

6.  Unlocking capacities of genomics for the COVID-19 response and future pandemics.

Authors:  Sergey Knyazev; Karishma Chhugani; Varuni Sarwal; Ram Ayyala; Harman Singh; Smruthi Karthikeyan; Dhrithi Deshpande; Pelin Icer Baykal; Zoia Comarova; Angela Lu; Yuri Porozov; Tetyana I Vasylyeva; Joel O Wertheim; Braden T Tierney; Charles Y Chiu; Ren Sun; Aiping Wu; Malak S Abedalthagafi; Victoria M Pak; Shivashankar H Nagaraj; Adam L Smith; Pavel Skums; Bogdan Pasaniuc; Andrey Komissarov; Christopher E Mason; Eric Bortz; Philippe Lemey; Fyodor Kondrashov; Niko Beerenwinkel; Tommy Tsan-Yuk Lam; Nicholas C Wu; Alex Zelikovsky; Rob Knight; Keith A Crandall; Serghei Mangul
Journal:  Nat Methods       Date:  2022-04       Impact factor: 47.990

7.  Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.

Authors:  Anthony P West; Joel O Wertheim; Jade C Wang; Tetyana I Vasylyeva; Jennifer L Havens; Moinuddin A Chowdhury; Edimarlyn Gonzalez; Courtney E Fang; Steve S Di Lonardo; Scott Hughes; Jennifer L Rakeman; Henry H Lee; Christopher O Barnes; Priyanthi N P Gnanapragasam; Zhi Yang; Christian Gaebler; Marina Caskey; Michel C Nussenzweig; Jennifer R Keeffe; Pamela J Bjorkman
Journal:  bioRxiv       Date:  2021-04-22

8.  Accounting for spatial sampling patterns in Bayesian phylogeography.

Authors:  Stéphane Guindon; Nicola De Maio
Journal:  Proc Natl Acad Sci U S A       Date:  2021-12-28       Impact factor: 11.205

9.  Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae.

Authors:  Adrian Viehweger; Christian Blumenscheit; Norman Lippmann; Kelly L Wyres; Christian Brandt; Jörg B Hans; Martin Hölzer; Luiz Irber; Sören Gatermann; Christoph Lübbert; Mathias W Pletz; Kathryn E Holt; Brigitte König
Journal:  Microb Genom       Date:  2021-12

Review 10.  COVID-19, the first pandemic in the post-genomic era.

Authors:  Lucy van Dorp; Charlotte J Houldcroft; Damien Richard; François Balloux
Journal:  Curr Opin Virol       Date:  2021-07-13       Impact factor: 7.090
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