ArticleMolecular biology and evolution2016
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed.
- Rapid Phylogeographic Inference of Regional Epidemic Dynamics for Routine Genomic Surveillance.Research square · 2026Article
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- Optimal control and the dynamics of ancestral lineages.Genetics · 2026Article
- SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.Nature communications · 2026Article
- The Phylodynamic Threshold of Measurably Evolving Populations.Molecular biology and evolution · 2026Article
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
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- Age-dependent Phylodynamics with Application to Single-cell Lineage Trees.Molecular biology and evolution · 2026Article
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- Exploring cooperation among social pathogens: a computational perspective.FEMS microbiology reviews · 2026Review
- Assessing the impact of Enhanced-Case-Finding on tuberculosis case notifications and transmission in The Gambia using epidemiological and phylodynamic approaches.Open research Europe · 2026Article
- Introduction and inter-species transmission dynamics of high pathogenicity avian influenza H5N1 viruses in Japan 2021-25.Virus evolution · 2026Article
- phyddle: Software for Exploring Phylogenetic Models with Deep Learning.Systematic biology · 2025Article
- Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.medRxiv : the preprint server for health sciences · 2025Article
- Inferring Cell Differentiation Dynamics with Unobserved Progenitors.bioRxiv : the preprint server for biology · 2025Article
- Zoonotic hepatitis E virus spreads through environmental routes in pig herds - A phylodynamic analysis.PLoS pathogens · 2025Article
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.PLoS computational biology · 2025Article
41 more citing papers are in PubMed but not listed here.
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth-death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.
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