ArticleNucleic acids research2011
Allele dynamics plots for the study of evolutionary dynamics in viral populations.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Influenza vaccine strain selection with an AI-based evolutionary and antigenicity model.Nature medicine · 2025Article
- In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 variants of interest.Nature communications · 2025Article
- Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations.Nature communications · 2024Article
- Antigenic characterization of influenza and SARS-CoV-2 viruses.Analytical and bioanalytical chemistry · 2022Review
- Article
- Advances in Development and Application of Influenza Vaccines.Frontiers in immunology · 2021Review
- Modeling the selective advantage of new amino acids on the hemagglutinin of H1N1 influenza viruses using their patient age distributions.Virus evolution · 2021Article
- Eleven grand challenges in single-cell data science.Genome biology · 2020Review
- Structures and functions linked to genome-wide adaptation of human influenza A viruses.Scientific reports · 2019Article
- Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.Viruses · 2018Article
- Models for predicting the evolution of influenza to inform vaccine strain selection.Human vaccines & immunotherapeutics · 2018Review
- Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.Scientific reports · 2018Article
- Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model.Scientific reports · 2016Article
- Selection of antigenically advanced variants of seasonal influenza viruses.Nature microbiology · 2016Article
- Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses.Virus evolution · 2016Article
- nextflu: real-time tracking of seasonal influenza virus evolution in humans.Bioinformatics (Oxford, England) · 2015Article
- Computational prediction of vaccine strains for human influenza A (H3N2) viruses.Journal of virology · 2014Article
- The maintenance of sex: Ronald Fisher meets the Red Queen.BMC evolutionary biology · 2013Article
- Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection.PLoS pathogens · 2012Article
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2 authors.
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Abstract
Phylodynamic techniques combine epidemiological and genetic information to analyze the evolutionary and spatiotemporal dynamics of rapidly evolving pathogens, such as influenza A or human immunodeficiency viruses. We introduce 'allele dynamics plots' (AD plots) as a method for visualizing the evolutionary dynamics of a gene in a population. Using AD plots, we propose how to identify the alleles that are likely to be subject to directional selection. We analyze the method's merits with a detailed study of the evolutionary dynamics of seasonal influenza A viruses. AD plots for the major surface protein of seasonal influenza A (H3N2) and the 2009 swine-origin influenza A (H1N1) viruses show the succession of substitutions that became fixed in the evolution of the two viral populations. They also allow the early identification of those viral strains that later rise to predominance, which is important for the problem of vaccine strain selection. In summary, we describe a technique that reveals the evolutionary dynamics of a rapidly evolving population and allows us to identify alleles and associated genetic changes that might be under directional selection. The method can be applied for the study of influenza A viruses and other rapidly evolving species or viruses.
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