Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data

(2021) Susana Posada-Céspedes et al.   BIOINFORMATICS

SARS-CoV-2 evolution during treatment of chronic infection

(2021) Steven A. Kemp et al.   NATURE

Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2

(2021) Amit Singh et al.   Scientific Reports

Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization

(2021) Pengfei Wang et al.   Cell Host & Microbe

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

(2021) Nuno R. Faria et al.   SCIENCE

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

(2021) Emma B. Hodcroft et al.   NATURE

Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

(2021) Daniel Lule Bugembe et al.   Nature Microbiology

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

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

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application

(2020) Stephen A. Lauer et al.   ANNALS OF INTERNAL MEDICINE

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

(2020) Markus Hoffmann et al.   MOLECULAR CELL

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

A need for open public data standards and sharing in light of COVID-19

(2020) Lauren Gardner et al.   LANCET INFECTIOUS DISEASES

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

(2020) Bas B. Oude Munnink et al.   NATURE MEDICINE

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

(2020) Andrew Rambaut et al.   Nature Microbiology

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

(2020) Leonid Yurkovetskiy et al.   CELL

A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture

(2020) Jalees A. Nasir et al.   Viruses-Basel

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

(2020) Philippe Lemey et al.   Nature Communications

Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases

(2020) Andrew William Byrne et al.   BMJ Open

Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

(2020) Bina Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

(2019) Nathan D. Grubaugh et al.   CELL

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

(2015) Guy Baele et al.   SYSTEMATIC BIOLOGY

Multiyear Persistence of 2 Pandemic A/H1N1 Influenza Virus Lineages in West Africa

(2014) Martha I. Nelson et al.   JOURNAL OF INFECTIOUS DISEASES

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

(2012) M. S. Gill et al.   MOLECULAR BIOLOGY AND EVOLUTION

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Bayesian analysis of elapsed times in continuous-time Markov chains

(2010) Marco A. R. Ferreira et al.   CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology