Temporal signal and the phylodynamic threshold of SARS-CoV-2
S Duchene, L Featherstone… - Virus …, 2020 - academic.oup.com
The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome
sequence data have been generated and made publicly available in near real time. Early …
sequence data have been generated and made publicly available in near real time. Early …
Trait‐dependent diversification in angiosperms: Patterns, models and data
Variation in species richness across the tree of life, accompanied by the incredible variety of
ecological and morphological characteristics found in nature, has inspired many studies to …
ecological and morphological characteristics found in nature, has inspired many studies to …
Epidemiological inference from pathogen genomes: a review of phylodynamic models and applications
LA Featherstone, JM Zhang, TG Vaughan… - Virus …, 2022 - academic.oup.com
Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology,
and statistical inference. It has also experienced more intense application than ever before …
and statistical inference. It has also experienced more intense application than ever before …
The origin and early spread of SARS-CoV-2 in Europe
SA Nadeau, TG Vaughan, J Scire… - Proceedings of the …, 2021 - National Acad Sciences
The investigation of migratory patterns during the SARS-CoV-2 pandemic before spring
2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border …
2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border …
Deep learning and likelihood approaches for viral phylogeography converge on the same answers whether the inference model is right or wrong
Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology.
Likelihood-based methods fit models to phylogenies to draw inferences about the …
Likelihood-based methods fit models to phylogenies to draw inferences about the …
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks
Widely applicable, accurate and fast inference methods in phylodynamics are needed to
fully profit from the richness of genetic data in uncovering the dynamics of epidemics …
fully profit from the richness of genetic data in uncovering the dynamics of epidemics …
The occurrence birth–death process for combined-evidence analysis in macroevolution and epidemiology
Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model
parameters, and more recently, the number of lineages through time, based on molecular …
parameters, and more recently, the number of lineages through time, based on molecular …
Bayesian phylodynamics reveals the transmission dynamics of avian influenza A (H7N9) virus at the human–live bird market interface in China
In 2013 to 2017, avian influenza A (H7N9) virus has caused five severe epidemic waves of
human infections in China. The role of live bird markets (LBMs) in the transmission dynamics …
human infections in China. The role of live bird markets (LBMs) in the transmission dynamics …
Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe
Abstract In winter 2016–7, Europe was severely hit by an unprecedented epidemic of highly
pathogenic avian influenza viruses (HPAIVs), causing a significant impact on animal health …
pathogenic avian influenza viruses (HPAIVs), causing a significant impact on animal health …
Phylodynamic signatures in the emergence of community-associated MRSA
Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have
emerged in many geographically distinct regions around the world during the past 30 y …
emerged in many geographically distinct regions around the world during the past 30 y …