RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning

McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks

(2023) Lun Li et al.   BRIEFINGS IN BIOINFORMATICS

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

(2023) Karthik Gangavarapu et al.   NATURE METHODS

On the collection and integration of SARS-CoV-2 genome data

(2023) Lina Ma et al.   Biosafety and Health

ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time

(2022) Luca Cilibrasi et al.   BIOINFORMATICS

Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

(2022) Philip L. Tzou et al.   PLoS One

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

(2022) Fritz Obermeyer et al.   SCIENCE

Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer

(2022) Derek W Wright et al.   Virus Evolution

Pandemic-Scale Phylogenomics Reveals The SARS-CoV-2 Recombination Landscape

(2022) Yatish Turakhia et al.   NATURE

VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2

(2022) Zhi-Jian Zhou et al.   BRIEFINGS IN BIOINFORMATICS

Sierra SARS-CoV-2 sequence and antiviral resistance analysis program

(2022) Philip L. Tzou et al.   JOURNAL OF CLINICAL VIROLOGY

CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants

(2021) Intikhab Alam et al.   LANCET INFECTIOUS DISEASES

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

(2021) Albert Tian Chen et al.   eLife

SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence

(2021) Thi Loi Dao et al.   Journal of Clinical Medicine

Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

(2021) Áine O’Toole et al.   Virus Evolution

CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants

(2021) Chaoran Chen et al.   BIOINFORMATICS

Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

(2021) Haibo Wu et al.   Cell Host & Microbe

The global epidemic of SARS‐CoV‐2 variants and their mutational immune escape

(2021) Dandan Tian et al.   JOURNAL OF MEDICAL VIROLOGY

VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes

(2021) Qinglan Sun et al.   NUCLEIC ACIDS RESEARCH

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters

(2020) Qi Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

(2020) Yanchun Peng et al.   NATURE IMMUNOLOGY

SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition

(2020) Annika Nelde et al.   NATURE IMMUNOLOGY

ViruSurf: an integrated database to investigate viral sequences

(2020) Arif Canakoglu et al.   NUCLEIC ACIDS RESEARCH

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

(2020) Shuhui Song et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

RDP5: A computer program for analysing recombination in, and removing signals of recombination from, nucleotide sequence datasets

(2020) Darren P Martin et al.   Virus Evolution

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data

(2018) Wenyu Shi et al.   NUCLEIC ACIDS RESEARCH

Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm

(2017) Ha Minh Lam et al.   MOLECULAR BIOLOGY AND EVOLUTION

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH