ArticleProceedings of the National Academy of Sciences of the United States of America2013
Topology of viral evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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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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Who cites it
68 citing papers in PubMed.
- Uncovering precision phenotype-biomarker associations in traumatic brain injury using topological data analysis.PloS one · 2017Trial
- Homological scaffolds of brain functional networks.Journal of the Royal Society, Interface · 2014Trial
- TopClust: Topological-based analysis of scRNA-seq data for data-driven identification of clusters and core cluster cells.Biophysical journal · 2026Article
- Node persistence from topological data analysis reveals changes in brain functional connectivity.Patterns (New York, N.Y.) · 2026Article
- Topological data analysis and topological deep learning beyond persistent homology: a review.Artificial intelligence review · 2026Article
- Global dynamics of avian influenza: a twenty-year analysis of highly pathogenic viruses linking the Caspian Basin, Eurasia and Africa sectors (2005-2025).Frontiers in cellular and infection microbiology · 2026Review
- A Review of Topological Data Analysis and Topological Deep Learning in Molecular Sciences.Journal of chemical information and modeling · 2025Review
- A novel method for subgroup discovery in precision medicine based on topological data analysis.BMC medical informatics and decision making · 2025Article
- A distribution-guided Mapper algorithm.BMC bioinformatics · 2025Article
- Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.Frontiers in microbiology · 2025Article
- Persistent Mayer Dirac.Journal of physics. Complexity · 2024Article
- Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.Bulletin of mathematical biology · 2024Article
- Article
- A universal null-distribution for topological data analysis.Scientific reports · 2023Article
- Using machine learning to detect coronaviruses potentially infectious to humans.Scientific reports · 2023Article
- The arithmetic topology of genetic alignments.Journal of mathematical biology · 2023Article
- Article
- Genomics data analysis via spectral shape and topology.PloS one · 2023Article
- An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis.Nature communications · 2022Article
- Topological data analysis in biomedicine: A review.Journal of biomedical informatics · 2022Review
8 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
The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate.
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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.