Research graph
References from COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences. Local targets link to admitted publications; unresolved targets remain external evidence.
Nextclade: clade assignment, mutation calling and quality control for viral genomes
10.21105/joss.03773 · 2021 · External reference
Superspreading genomes
10.1126/science.abg0100 · 2021 · External reference
Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021
10.2807/1560-7917.es.2021.26.28.2100573 · 2021 · External reference
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
10.1371/journal.pcbi.1003537 · 2014 · External reference
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
10.1093/bioinformatics/btab856 · 2022 · External reference
Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
10.7554/elife.82538 · 2023 · External reference
A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics
10.1093/aje/kwt133 · 2013 · External reference
COVFlow: performing virus phylodynamics analyses from selected SARS-CoV-2 genome sequences
10.5281/zenodo.8016623 · 2023 · External reference
COVFlow: viral phylodynamics pipeline
10.5281/zenodo.8425036 · 2023 · External reference
10.24072/pcjournal.40 · 2021 · Admitted local publication
Data, disease and diplomacy: GISAID's innovative contribution to global health
10.1002/gch2.1018 · 2017 · External reference
Introductions and early spread of SARS-CoV-2 in France
10.2807/1560-7917.es.2020.25.26.2001200 · 2020 · External reference
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
10.1038/s41592-023-01769-3 · 2023 · External reference
Unifying the epidemiological and evolutionary dynamics of pathogens
10.1126/science.1090727 · 2004 · External reference
Bioconda: sustainable and comprehensive software distribution for the life sciences
10.1038/s41592-018-0046-7 · 2018 · External reference
Accounting for spatial sampling patterns in Bayesian phylogeography
10.1073/pnas.2105273118 · 2021 · External reference
Nextstrain: real-time tracking of pathogen evolution
10.1093/bioinformatics/bty407 · 2018 · External reference
The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study
10.1093/ve/vew003 · 2016 · External reference
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
10.21105/joss.02906 · 2021 · External reference
Estimating effective population size changes from preferentially sampled genetic sequences
10.1371/journal.pcbi.1007774 · 2020 · External reference
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
10.1093/molbev/mst010 · 2013 · External reference
GISAID’s Role in Pandemic Response
10.46234/ccdcw2021.255 · 2021 · External reference
"Snakemake—a scalable bioinformatics workflow engine"
10.1093/bioinformatics/bts480 · 2012 · External reference
A pipeline to select SARS-CoV-2 sequences for reliable phylodynamic analyses
10.24072/pci.genomics.100239 · 2023 · External reference
Fundamental Identifiability Limits in Molecular Epidemiology
10.1093/molbev/msab149 · 2021 · External reference
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
10.1126/science.abf2946 · 2021 · External reference
Insights from SARS-CoV-2 sequences
10.1126/science.abf3995 · 2021 · External reference
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
10.1093/molbev/msaa015 · 2020 · External reference
"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool"
10.1093/ve/veab064 · 2021 · External reference
Phylodynamic Analysis 176 genomes 6 Mar 2020
2020 · External reference
"Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7"
10.1093/sysbio/syy032 · 2018 · External reference
TreeTime: Maximum-likelihood phylodynamic analysis
10.1093/ve/vex042 · 2018 · External reference
Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022
10.3201/eid2807.220033 · 2022 · External reference
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
10.1073/pnas.1207965110 · 2013 · External reference
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
10.1093/ve/vey016 · 2018 · External reference
Improved inference of time-varying reproduction numbers during infectious disease outbreaks
10.1016/j.epidem.2019.100356 · 2019 · External reference
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
10.1016/j.cell.2020.11.020 · 2021 · External reference
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
10.1126/science.abj4336 · 2021 · External reference
Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study
10.1016/s0140-6736(20)30566-3 · 2020 · External reference
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
10.1126/science.abf2946 · 2021 · External reference
