The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Topology of viral evolution
Open accessAbstract
Significance: Evolution is mediated not only by random mutations over a number of generations (vertical evolution), but also through the mixture of genomic material between individuals of different lineages (horizontal evolution). The standard evolutionary representation, the phylogenetic tree, faithfully represents the former but not the latter scenario. Although many elaborations have been developed to address this issue, there is still no agreed-upon method of incorporating both vertical and horizontal evolution. Here, we present an alternative strategy based on algebraic topology to study evolution. This method extends beyond the limits of a tree to capture directly even complex horizontal exchanges between multiple parental strains, as well as uncover broader reticulate patterns, including the segregation of segments during reassortment.
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In the citing paper
“In the case of strict clonal evolution, all information is captured by the zero-dimensional homology.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“However, the metric space produced by using the concatenated sequences did produce significant onedimensional homology, which would preclude phylogeny as a complete explanation.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“When each distinct segment was studied, there was no higher-dimensional behaviour.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“By performing persistent homological calculations on simulations, it was observed that a lower bound for the recombination/reassortment rate was obtained by studying the counts of the number of bars in the corresponding barcode.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“The type of exchange of genomic material can be catalogued by the topology of the genomic data.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“Persistent homology shows higher-dimensional homology groups capturing some of the complex recombinant structures.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“when analysing the homology of avian influenza A, it was shown that several segments, containing the genes that encode the polymerases, are more likely to co-segregate together”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
In the citing paper
“In the cases studied, these occurrences were consistent with the known horizontal transfer mechanisms in these situations.”
From Topological pattern recognition for point cloud data (2014) · cites this paper as Chan et al. (2013)
Citations
Cites
Application of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,895
Wooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,093
Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus
Gao, R., Cao, B., Hu, Y., Feng, Z., Wang, D., Hu, W., Chen, J., Jie, Z., Qiu, H., Xu, K., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1304459 · Cited by 2,310
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888
Smith, J. M., Smith, N. H., O'Rourke, M., & Spratt, B. G. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.10.4384 · Cited by 1,802
Analyzing the mosaic structure of genes
Smith, J. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00182389 · Cited by 1,630
Zomorodian, A., & Carlsson, G. (2005) · Discrete & Computational Geometry · doi:10.1007/s00454-004-1146-y · Cited by 1,591
Self-citationFouchier, R. A. M., Munster, V. J., Wallensten, A., Bestebroer, T. M., Herfst, S., Smith, D. J., Rimmelzwaan, G. F., Olsén, B., & Osterhaus, A. D. M. E. (2005) · Journal of Virology · doi:10.1128/jvi.79.5.2814-2822.2005 · Cited by 1,565
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Bruen, T. C., Philippe, H., & Bryant, D. (2006) · Genetics · doi:10.1534/genetics.105.048975 · Cited by 1,366
Drummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059
Cited by
Sorted by citations
A roadmap for the computation of persistent homology
Otter, N., Porter, M. A., Tillmann, U., Grindrod, P., & Harrington, H. A. (2017) · EPJ Data Science · doi:10.1140/epjds/s13688-017-0109-5 · Cited by 769
Homological scaffolds of brain functional networks
Petri, G., Expert, P., Turkheimer, F., Carhart-Harris, R., Nutt, D., Hellyer, P. J., & Vaccarino, F. (2014) · Journal of The Royal Society Interface · doi:10.1098/rsif.2014.0873 · Cited by 675
Two’s company, three (or more) is a simplex
Giusti, C., Ghrist, R., & Bassett, D. S. (2016) · Journal of Computational Neuroscience · doi:10.1007/s10827-016-0608-6 · Cited by 426
What are higher-order networks?
Bick, C., Gross, E., Harrington, H. A., & Schaub, M. T. (2023) · SIAM Review · doi:10.1137/21m1414024 · Cited by 420
Clique topology reveals intrinsic geometric structure in neural correlations
Giusti, C., Pastalkova, E., Curto, C., & Itskov, V. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1506407112 · Cited by 381
Metadata
- Authors
- Chan, J. M., Carlsson, G., & Rabadan, R.
- Affiliations
- Columbia University (US)
- Stanford University (US)
- Center for Computational Biology and Bioinformatics and
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-10-29
- Volume
- 110
- Issue
- 46
- Pages
- 18566-18571
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3831954
- OpenAlex
- W2107385756
- Cited by
- 269
- References
- 46
- Citations by year
- 2026: 10 · 2025: 12 · 2024: 15 · 2023: 27 · 2022: 14 · 2021: 37 · 2020: 28 · 2019: 23 · 2018: 18 · 2017: 29 · 2016: 27 · 2015: 18 · 2014: 10 · 2013: 1
- FWCI
- 12.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0905823, 0964242)
- National Institutes of Health (W81XWH, CA121852, U54-CA121852)
- National Cancer Institute (U54CA121852, U54CA149145, I-U54_CA149145-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
- Keywords
- reticulate evolution, viral evolution, algebraic topology, phylogenetic tree, reassortment, recombination, RNA viruses, H7N9 avian influenza, HIV-1 recombinants, clonal evolution
- MeSH terms
- Base Sequence, Classification, Computer Simulation, Models, Genetic, Phylogeny, HIV-1, Reassortant Viruses, Sequence Homology, Evolution, Molecular, Computational Biology, Gene Transfer, Horizontal, Principal Component Analysis, Influenza A Virus, H1N1 Subtype, Molecular Sequence Annotation, Influenza A Virus, H7N9 Subtype
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