ArticlePLoS computational biology2020
Estimating effective population size changes from preferentially sampled genetic sequences.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus.bioRxiv : the preprint server for biology · 2026Article
- Genetic diversity of Mycobacterium bovis in dairy products and cattle tissues from northwest Iran using a 12-locus MIRU-VNTR approach.Scientific reports · 2026Article
- Tracing Dengue's Evolutionary and Phylogenetic Pathways.Current topics in microbiology and immunology · 2026Review
- Phylodynamic analyses reveal persistence and extensive intermixing of Usutu virus in the Netherlands.Virus evolution · 2026Article
- BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference.Nature methods · 2025Article
- Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling.PLoS computational biology · 2025Article
- Molecular Evolutionary Analyses ofMicroorganisms · 2024Article
- Interrogating Genomes and Geography to Unravel Multiyear Vesicular Stomatitis Epizootics.Viruses · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.PLoS computational biology · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
- adaPop: Bayesian inference of dependent population dynamics in coalescent models.PLoS computational biology · 2023Article
- Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data.Virology journal · 2022Article
- Statistical Challenges in Tracking the Evolution of SARS-CoV-2.Statistical science : a review journal of the Institute of Mathematical Statistics · 2022Article
- Adaptive Preferential Sampling in Phylodynamics With an Application to SARS-CoV-2.Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America · 2022Article
- Distance metrics for ranked evolutionary trees.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences.Molecular biology and evolution · 2020Article
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Authors and funding
5 authors.
Funding
Abstract
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through time and the distribution of the sampling times depends on the effective population size, explicit statistical modeling of sampling times improves population size estimation. Previous work assumed that the genealogy relating sampled sequences is known and modeled sampling times as an inhomogeneous Poisson process with log-intensity equal to a linear function of the log-transformed effective population size. We improve this approach in two ways. First, we extend the method to allow for joint Bayesian estimation of the genealogy, effective population size trajectory, and other model parameters. Next, we improve the sampling time model by incorporating additional sources of information in the form of time-varying covariates. We validate our new modeling framework using a simulation study and apply our new methodology to analyses of population dynamics of seasonal influenza and to the recent Ebola virus outbreak in West Africa.
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