Integrating fossil observations into phylogenetics using the fossilized birth–death model
Over the past decade, a new set of methods for estimating dated trees has emerged.
Originally referred to as the fossilized birth–death (FBD) process, this single model has …
Originally referred to as the fossilized birth–death (FBD) process, this single model has …
Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues
A lot of what we know about past speciation and extinction dynamics is based on statistically
fitting birth–death processes to phylogenies of extant species. Despite their wide use, the …
fitting birth–death processes to phylogenies of extant species. Despite their wide use, the …
Fundamental identifiability limits in molecular epidemiology
Viral phylogenies provide crucial information on the spread of infectious diseases, and many
studies fit mathematical models to phylogenetic data to estimate epidemiological parameters …
studies fit mathematical models to phylogenetic data to estimate epidemiological parameters …
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 …
[HTML][HTML] Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts
Birth-death processes have given biologists a model-based framework to answer questions
about changes in the birth and death rates of lineages in a phylogenetic tree. Therefore birth …
about changes in the birth and death rates of lineages in a phylogenetic tree. Therefore birth …
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 …
Infectious disease phylodynamics with occurrence data
LA Featherstone, F Di Giallonardo… - Methods in Ecology …, 2021 - Wiley Online Library
Phylodynamic models use pathogen genome sequence data to infer epidemiological
dynamics. With the increasing genomic surveillance of pathogens, especially during the …
dynamics. With the increasing genomic surveillance of pathogens, especially during the …
[HTML][HTML] Statistical challenges in tracking the evolution of SARS-CoV-2
Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and
evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular …
evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular …
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
Accurately estimating the effective reproduction number (Rt) of a circulating pathogen is a
fundamental challenge in the study of infectious disease. The fields of epidemiology and …
fundamental challenge in the study of infectious disease. The fields of epidemiology and …
[HTML][HTML] A computationally tractable birth-death model that combines phylogenetic and epidemiological data
Inferring the dynamics of pathogen transmission during an outbreak is an important problem
in infectious disease epidemiology. In mathematical epidemiology, estimates are often …
in infectious disease epidemiology. In mathematical epidemiology, estimates are often …