ArticleEpidemics2015
Eight challenges in phylodynamic inference.
Article in Epidemics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
- Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses.PloS one · 2026Article
- Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis.Virus evolution · 2026Article
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Article
- Visitors Without Passports: A Synthesis of Invasion Routes and Phylogeographic Patterns in the Asian Tiger Mosquito Based on Single-Locus Genetic Analyses.Zoological studies · 2025Article
- Transdisciplinary training to address challenges in genomic epidemiology of infectious diseases.Frontiers in public health · 2025Article
- Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.Virus evolution · 2025Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.PLoS computational biology · 2024Article
- Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis.bioRxiv : the preprint server for biology · 2024Article
- Review
- Identifying changes in viral fitness using population genetic structure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England.PLoS pathogens · 2024Article
- No evidence that a transmissible cancer has shifted from emergence to endemism in Tasmanian devils.Royal Society open science · 2024Article
- Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages.Virus evolution · 2024Article
- Emerging advances in biosecurity to underpin human, animal, plant, and ecosystem health.iScience · 2023Review
- Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2023Article
- Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics.PLoS pathogens · 2023Review
- Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.Viruses · 2023Review
23 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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Abstract
The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data.
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