ArticleVirus evolution2023
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance.
Article in Virus evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Effectiveness of non-pharmaceutical interventions as implemented in the UK during the COVID-19 pandemic: a rapid review.Journal of public health (Oxford, England) · 2025Pooled it
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- Quantifying the predictability of evolution by analysis of coalescent rate variation.Molecular biology and evolution · 2026Article
- Phylogenomic analysis of a methicillin-resistantMicrobial genomics · 2026Article
- Enhanced invasiveness promotes the dominance of a widely-distributed carbapenem-resistant virulence-plasmid-carrying Klebsiella pneumoniae sublineage.Nature communications · 2026Article
- DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.Molecular biology and evolution · 2026Article
- South Asian origin and global transmission history ofmSystems · 2025Article
- Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom.Virus evolution · 2025Article
- Non-pharmaceutical interventions to reduce COVID-19 transmission in the UK: a rapid mapping review and interactive evidence gap map.Journal of public health (Oxford, England) · 2024Review
- Rapid expansion and international spread of M1Nature communications · 2024Article
- Spatiotemporal evolution of SARS-CoV-2 in the Bangkok metropolitan region, Thailand, 2020-2022: implications for future outbreak preparedness.Microbial genomics · 2023Article
- Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Inference of effective population size from genomic data can provide unique information about demographic history and, when applied to pathogen genetic data, can also provide insights into epidemiological dynamics. The combination of nonparametric models for population dynamics with molecular clock models which relate genetic data to time has enabled phylodynamic inference based on large sets of time-stamped genetic sequence data. The methodology for nonparametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on nonparametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. Our methodology is implemented in a new R package entitled
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.