ReviewVirus evolution2022
Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.
Review in Virus evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- Future-use consent and human virome research: ethical challenges.Journal of virology · 2026Review
- Leveraging synthetic and genetic data to improve epidemic forecasting.PLoS computational biology · 2026Article
- Hidden Burden of a Measles Outbreak Revealed by Genomic and Transmission Models.medRxiv : the preprint server for health sciences · 2026Article
- PhyloCNN: Improving Tree Representation and Neural Network Architecture for Deep Learning from Trees in Phylodynamics and Diversification Studies.Systematic biology · 2026Article
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
- e3SIM: Epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.Methods in ecology and evolution · 2026Article
- Ancestral state reconstruction with discrete characters using deep learning.bioRxiv : the preprint server for biology · 2026Article
- Introduction and inter-species transmission dynamics of high pathogenicity avian influenza H5N1 viruses in Japan 2021-25.Virus evolution · 2026Article
- Phylo-rs: an extensible phylogenetic analysis library in rust.BMC bioinformatics · 2025Article
- Novel Adomaviruses Associated with Blotchy Bass Syndrome in Black Basses (bioRxiv : the preprint server for biology · 2025Article
- How does date-rounding affect phylodynamic inference for public health?PLoS computational biology · 2025Article
- Article
- Tracking Seasonal Influenza Trends in South Tyrol During 2022/2023 Using Genomic Surveillance Data.Influenza and other respiratory viruses · 2025Article
- Looking back into the Hepatitis C Virus epidemic dynamics from Unnao, India through phylogenetic approach.PloS one · 2025Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- Applying Field and Genomic Epidemiology Methods to Investigate Transmission Networks of Highly Pathogenic Avian Influenza A (H5N1) in Domestic Poultry in British Columbia, Canada (2022-2023).Transboundary and emerging diseases · 2025Article
- Novel adomaviruses associated with blotchy bass syndrome in black basses (Micropterus spp.).PloS one · 2025Article
- Exploring SNP filtering strategies: the influence of strict vs soft core.Microbial genomics · 2025Article
- Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression.Systematic biology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and statistical inference. It has also experienced more intense application than ever before amid the SARS-CoV-2 pandemic. In light of this, we present a review of phylodynamic models beginning with foundational models and assumptions. Our target audience is public health researchers, epidemiologists, and biologists seeking a working knowledge of the links between epidemiology, evolutionary models, and resulting epidemiological inference. We discuss the assumptions linking evolutionary models of pathogen population size to epidemiological models of the infected population size. We then describe statistical inference for phylodynamic models and list how output parameters can be rearranged for epidemiological interpretation. We go on to cover more sophisticated models and finish by highlighting future directions.
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