ArticleNature methods2022
Unlocking capacities of genomics for the COVID-19 response and future pandemics.
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Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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0cells of the map it votes in
30citing papers in PubMed, 1 pooled it
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What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review.Epidemiology and infection · 2026Pooled it
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Inequities and global declines in SARS-CoV-2 genomic data availability hinder response to emerging variants.Npj viruses · 2026Review
- Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop.PLoS computational biology · 2026Article
- The Era of Large-Scale Data in Biological Sciences.Advances in experimental medicine and biology · 2026Review
- The value of large-scale programmes in human genomics.European journal of human genetics : EJHG · 2025Article
- A rapid evaluation of the UK Health Security Agency's New Variant Assessment Platform global genomic surveillance programme.PLOS global public health · 2025Article
- Detection of Long-Distance Transmission Events During the CSF Epidemic in Japan Using Whole-Genome-Sequence Data.Transboundary and emerging diseases · 2025Article
- Metagenomic next generation sequencing of plasma RNA for diagnosis of unexplained, acute febrile illness in Uganda.PLoS neglected tropical diseases · 2024Article
- Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks.Nature communications · 2024Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater.International journal of molecular sciences · 2023Article
- Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology.Antibiotics (Basel, Switzerland) · 2023Review
- COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2.Briefings in bioinformatics · 2023Article
- Immune landscape and redox imbalance during neurological disorders in COVID-19.Cell death & disease · 2023Review
- LAPIS is a fast web API for massive open virus sequencing data.BMC bioinformatics · 2023Article
- Genomic surveillance identifies potential risk factors for SARS-CoV-2 transmission at a mid-sized university in a small rural town.Scientific reports · 2023Article
- Systematic Guidelines for Effective Utilization of COVID-19 Databases in Genomic, Epidemiologic, and Clinical Research.Viruses · 2023Review
- Article
- SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs.Nature genetics · 2023Article
Corrections and comments
- Update of
Authors and funding
35 authors.
Sergey Knyazev *Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-0385-1831
Karishma Chhugani *Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-8764-9352
Varuni SarwalDepartment of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
Ram AyyalaDepartment of Translational Biomedical Informatics, University of Southern California, Los Angeles, CA, USA.
Harman SinghDepartment of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India.
Smruthi KarthikeyanDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Dhrithi DeshpandeDepartment of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
Pelin Icer BaykalDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Zoia ComarovaAstani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA.
Angela LuDepartment of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
Yuri PorozovWorld-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia.ORCID http://orcid.org/0000-0002-5450-3135
Tetyana I VasylyevaDepartment of Medicine, University of California, San Diego, La Jolla, CA, USA.
Joel O WertheimDepartment of Medicine, University of California, San Diego, La Jolla, CA, USA.
Braden T TierneyDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Charles Y ChiuDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-2915-2094
Ren SunDepartment of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.
Aiping WuInstitute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
Malak S AbedalthagafiGenomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
Victoria M PakEmory University, School of Nursing, Atlanta, GA, CA, USA.
Shivashankar H NagarajCentre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia.
Adam L SmithAstani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA.
Pavel SkumsDepartment of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA.ORCID http://orcid.org/0000-0003-4007-5624
Bogdan PasaniucDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Andrey KomissarovSmorodintsev Research Institute of Influenza, Saint Petersburg, Russia.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0002-1850-1642
Eric BortzDepartment of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, CA, USA.ORCID http://orcid.org/0000-0002-1376-0012
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium.ORCID http://orcid.org/0000-0003-2826-5353
Fyodor KondrashovInstitute of Science and Technology Austria, Klosterneuburg, Austria.
Niko BeerenwinkelDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.ORCID http://orcid.org/0000-0002-0573-6119
Tommy Tsan-Yuk LamState Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P.R. China.
Nicholas C WuDepartment of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Alex ZelikovskyDepartment of Computer Science, College of Art and Science, Georgia State University, Atlanta, GA, USA.
Rob KnightDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0975-9019
Keith A CrandallComputational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.ORCID http://orcid.org/0000-0002-0836-3389
Serghei MangulDepartment of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA. serghei.mangul@gmail.com.ORCID http://orcid.org/0000-0003-4770-3443
Funding
The Administrative CoreP20GM103395 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI STACY M. RASMUS · 2012 to 2026
$66.1MTechnology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Bryan Briney · 2018 to 2026
$32.0MJoint genomic and statistical analyses of schizophrenia and bipolar to decipher genetic susceptibilityR01MH115676 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Roel A Ophoff, Bogdan Pasaniuc · 2018 to 2026
$5.9MDefining the role of the RNA modification N6-methyladenosine in the hepatitis C virus lifecycleR01AI125416 · NIAID · DUKE UNIVERSITY · PI Stacy Michelle Horner · 2016 to 2026
$5.5MPRS Center for Admixed Populations (CAPE)U01HG011715 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI Eimear Elizabeth Kenny, Leslie A Lange · 2021 to 2026
$5.2MSupplement for MINI point-of-use deviceU01DA053941 · NIDA · UNIVERSITY OF MIAMI CORAL GABLES · PI MASON, CHRISTOPHER EDWARD, SCHURER, STEPHAN C · 2021 to 2022
$5.2MCollaborative multi-site project to speed the identification and management of rare genetic immune diseasesR01AI153827 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BUTTE, MANISH J, PASANIUC, BOGDAN · 2021 to 2025
$3.9MAutomation and Evaluation of Real-Time Transmission Network-Based HIV Prevention Services in New York CityR01AI135992 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WERTHEIM, JOEL OKRENT · 2018 to 2022
$3.6MMetagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantationR01AI151059 · NIAID · CORNELL UNIVERSITY · PI DADHANIA, DARSHANA, DE VLAMINCK, IWIJN · 2020 to 2024
$3.4MSequence-function relationship of influenza broadly neutralizing antibodiesR01AI167910 · NIAID · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Nicholas C. Wu · 2022 to 2026
$2.5MStatistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4MHigh-throughput identification of antibody features for sequence-based epitope predictionDP2AT011966 · NCCIH · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI WU, NICHOLAS C. · 2021 to 2024
$2.4MNCCIH NIH HHS DP2 AT011966NCEZID CDC HHS U01 CK000539NCI NIH HHS R21 CA241044NHGRI NIH HHS R01 HG009120NHGRI NIH HHS U01 HG011715NIAID NIH HHS R00 AI139445NIAID NIH HHS R01 AI125416NIAID NIH HHS R01 AI135992NIAID NIH HHS R01 AI151059NIAID NIH HHS R01 AI153044NIAID NIH HHS R01 AI153827NIAID NIH HHS R01 AI167910NIAID NIH HHS R21 AI129851NIAID NIH HHS U19 AI135995NIBIB NIH HHS R01 EB025022NIDA NIH HHS U01 DA053941NIGMS NIH HHS P20 GM103395NIMH NIH HHS R01 MH115676Wellcome TrustWellcome Trust 206298/Z/17/Z
Abstract
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COVID-19PandemicsGenomicsHumansSARS-CoV-2
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