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References from Early phylodynamics analysis of the COVID-19 epidemic in France. Local targets link to admitted publications; unresolved targets remain external evidence.
The proximal origin of SARS-CoV-2
10.1038/s41591-020-0820-9 · 2020 · External reference
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
10.1371/journal.pcbi.1003537 · External reference
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
10.1093/genetics/161.3.1307 · 2002 · External reference
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
10.1093/molbev/mss075 · 2012 · External reference
Temporal signal and the phylodynamic threshold of SARS-CoV-2
10.1093/ve/veaa061 · 2020 · External reference
Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing
10.1126/science.abb6936 · 2020 · External reference
Eight challenges in phylodynamic inference
10.1016/j.epidem.2014.09.001 · 2015 · External reference
Introductions and early spread of SARS-CoV-2 in France, 24 January to 23 March 2020
10.2807/1560-7917.es.2020.25.26.2001200 · 2020 · External reference
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
10.1126/science.1090727 · 2004 · External reference
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
10.1080/10635150390235520 · 2003 · External reference
Nextstrain: real-time tracking of pathogen evolution
10.1093/bioinformatics/bty407 · 2018 · External reference
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
10.1038/s41564-020-0695-z · 2020 · External reference
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model
10.1098/rsif.2013.1106 · 2014 · External reference
SMS: Smart Model Selection in PhyML
10.1093/molbev/msx149 · 2017 · External reference
Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia
10.1056/nejmoa2001316 · 2020 · External reference
Secondary attack rate and superspreading events for SARS-CoV-2
10.1016/s0140-6736(20)30462-1 · 2020 · External reference
RDP4: Detection and analysis of recombination patterns in virus genomes
10.1093/ve/vev003 · 2015 · External reference
Unresolved reference
External reference
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
10.1038/s41564-020-0770-5 · 2020 · External reference
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
10.1093/ve/vew007 · 2016 · External reference
Estimating the burden of SARS-CoV-2 in France
10.1126/science.abc3517 · 2020 · External reference
Unresolved reference
2020 · External reference
A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
10.1093/bioinformatics/18.1.115 · 2002 · External reference
Memory is key in capturing COVID-19 epidemiological dynamics
10.1016/j.epidem.2021.100459 · 2021 · External reference
Estimating the Basic Reproductive Number from Viral Sequence Data
10.1093/molbev/msr217 · 2012 · 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
Fast Dating Using Least-Squares Criteria and Algorithms
10.1093/sysbio/syv068 · 2015 · External reference
Viral Phylodynamics
10.1371/journal.pcbi.1002947 · 2013 · External reference
10.25561/77169
10.25561/77169 · External reference
How generation intervals shape the relationship between growth rates and reproductive numbers
10.1098/rspb.2006.3754 · 2006 · External reference
A new coronavirus associated with human respiratory disease in China
10.1038/s41586-020-2008-3 · 2020 · External reference
Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins
10.1038/s41586-020-2313-x · 2020 · External reference
A pneumonia outbreak associated with a new coronavirus of probable bat origin
10.1038/s41586-020-2012-7 · 2020 · External reference