Untangling introductions and persistence in COVID-19 resurgence in Europe

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

(2021) Louis du Plessis et al.   SCIENCE

Vaccination and non-pharmaceutical interventions for COVID-19: a mathematical modelling study

(2021) Sam Moore et al.   LANCET INFECTIOUS DISEASES

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

(2021) Emma B. Hodcroft et al.   NATURE

Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study

(2020) Marius Gilbert et al.   LANCET

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

(2020) Mandev S Gill et al.   MOLECULAR BIOLOGY AND 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

Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series

(2020) Merle M Böhmer et al.   LANCET INFECTIOUS DISEASES

A European roadmap out of the covid-19 pandemic

(2020) Martin McKee   BMJ-British Medical Journal

Mapping global variation in human mobility

(2020) Moritz U. G. Kraemer et al.   Nature Human Behaviour

Impact of lockdown on COVID-19 epidemic in Île-de-France and possible exit strategies

(2020) Laura Di Domenico et al.   BMC Medicine

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

(2020) Andrew Rambaut et al.   Nature Microbiology

The emergence of SARS-CoV-2 in Europe and North America

(2020) Michael Worobey et al.   SCIENCE

Phylogenetic analysis of SARS-CoV-2 data is difficult

(2020) Benoit Morel et al.   MOLECULAR BIOLOGY AND EVOLUTION

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

Hierarchical organization of urban mobility and its connection with city livability

(2019) Aleix Bassolas et al.   Nature Communications

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

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

(2017) Yuelong Shu et al.   Eurosurveillance

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

(2015) Guy Baele et al.   SYSTEMATIC BIOLOGY

Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography

(2014) Filip Bielejec et al.   SYSTEMATIC BIOLOGY

Split diversity in constrained conservation prioritization using integer linear programming

(2014) Olga Chernomor et al.   Methods in Ecology and Evolution

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

Graph hierarchies for phylogeography

(2013) G. B. Cybis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Fast, accurate and simulation-free stochastic mapping

(2008) V. N Minin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES