The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
Open accessAbstract
Phylogenetic trees can be used to infer the processes that generated them. Here, we introduce a model, the Bayesian birth–death skyline plot, which explicitly estimates the rate of transmission, recovery, and sampling and thus allows inference of the effective reproductive number directly from genetic data. Our method allows these parameters to vary through time in a piecewise fashion and is implemented within the B EAST 2 software framework. The method is a powerful alternative to the existing coalescent skyline plot, providing insight into the differing roles of incidence and prevalence in an epidemic. We apply this method to data from the United Kingdom HIV-1 epidemic and Egyptian hepatitis C virus (HCV) epidemic. The analysis reveals temporal changes of the effective reproductive number that highlight the effect of past public health interventions.
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Cites
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The role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt
Frank, C., Mohamed, M. K., Strickland, G. T., Lavanchy, D., Arthur, R. R., Magder, L. S., Khoby, T. E., Abdel-Wahab, Y., Ohn, E. S. A., Anwar, W., et al. (2000) · The Lancet · doi:10.1016/s0140-6736(99)06527-7 · Cited by 1,131
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Self-citation
Cited by
BEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527
Self-citationBEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556
Self-citationThe fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834
Self-citationBenson, R. B. J., Campione, N. E., Carrano, M. T., Mannion, P. D., Sullivan, C., Upchurch, P., & Evans, D. C. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001853 · Cited by 457
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03677-y · Cited by 425
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Metadata
- Authors
- Stadler, T., Kühnert, D., Bonhoeffer, S., & Drummond, A. J.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-12-17
- Volume
- 110
- Issue
- 1
- Pages
- 228-233
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2160253520
- Cited by
- 541
- References
- 6
- FWCI
- 9.39
- Type
- journal article
- Language
- en
- Open access
- green
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- Stadler, T., Kühnert, D., Bonhoeffer, S., & Drummond, A. J. (2013). Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1207965110
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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