ArticleMolecular biology and evolution2008
Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.
Article in Molecular biology and evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 405 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
405 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review.The Lancet. Microbe · 2025Pooled it
- Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.Viruses · 2022Trial
- HIV-1 variants are archived throughout infection and persist in the reservoir.PLoS pathogens · 2020Trial
- Phylodynamic analysis provides insights into genotype displacement of duck hepatitis A virus in China.Journal of veterinary science · 2026Article
- Divergent Thermal Reaction Norms of the Spontaneous Mutation Rate Among Populations of Chironomus riparius.Molecular ecology · 2026Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Emergence of distinct Streptococcus pyogenes emm1 and emm12 lineages in China.Nature microbiology · 2026Article
- Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health.PLoS neglected tropical diseases · 2026Article
- Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats.Nature microbiology · 2026Article
- Article
- torchtree: Flexible Phylogenetic Model Development and Inference Using PyTorch.Systematic biology · 2026Article
- H5N1 clade 2.3.2.1e lineage transition in Lao PDR during 2023-2024 associated with regional spread and human infection risk-associated receptor-binding features.Frontiers in public health · 2026Article
- Wild birds drive the introduction, maintenance, and spread of H5N1 clade 2.3.4.4b high pathogenicity avian influenza viruses in Spain, 2021-2022.Virus evolution · 2026Article
- Evolution and Spread of Regionally Adapted Newcastle Disease Virus Isolates From Live Bird Markets in Nigeria, 2023-2024.Transboundary and emerging diseases · 2026Article
- Genomic and Clinicopathological Characterization of a Reassortant HPAI H5N1 (Clade 2.3.4.4b) in an Endangered Cinereous Vulture (Aegypius monachus) in South Korea, 2026.Transboundary and emerging diseases · 2026Article
- Phylodynamic analysis reveals disparate transmission dynamics of Mycobacterium tuberculosis complex lineages in Botswana.Scientific reports · 2025Article
- Efficient Bayesian Phylogenetics under the Infinite Sites Model.bioRxiv : the preprint server for biology · 2025Article
- Temporal reconstruction of aMicrobial genomics · 2025Article
- Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades.Veterinary microbiology · 2025Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.bioRxiv : the preprint server for biology · 2025Article
345 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the demographic history of a population. Because researchers are rarely able to choose a priori a deterministic model describing effective population size dynamics for data at hand, nonparametric curve-fitting methods based on multiple change-point (MCP) models have been developed. We propose an alternative to change-point modeling that exploits Gaussian Markov random fields to achieve temporal smoothing of the effective population size in a Bayesian framework. The main advantage of our approach is that, in contrast to MCP models, the explicit temporal smoothing does not require strong prior decisions. To approximate the posterior distribution of the population dynamics, we use efficient, fast mixing Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. In a simulation study, we demonstrate that the proposed temporal smoothing method, named Bayesian skyride, successfully recovers "true" population size trajectories in all simulation scenarios and competes well with the MCP approaches without evoking strong prior assumptions. We apply our Bayesian skyride method to 2 real data sets. We analyze sequences of hepatitis C virus contemporaneously sampled in Egypt, reproducing all key known aspects of the viral population dynamics. Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons.
Indexed as
Identifiers
What OpenQuestion holds
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.