The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
Open accessAbstract
Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We present an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes. This leaves the distribution of selection parameters essentially unconstrained, and also allows sites experiencing positive and purifying selection to be identified orders of magnitude faster than by existing methods. We demonstrate that popular random effects likelihood methods can produce misleading results when sites assigned to the same site class experience different levels of positive or purifying selection--an unavoidable scenario when using a small number of site classes. Our Fast Unconstrained Bayesian AppRoximation (FUBAR) is unaffected by this problem, while achieving higher power than existing unconstrained (fixed effects likelihood) methods. The speed advantage of FUBAR allows us to analyze larger data sets than other methods: We illustrate this on a large influenza hemagglutinin data set (3,142 sequences). FUBAR is available as a batch file within the latest HyPhy distribution (http://www.hyphy.org), as well as on the Datamonkey web server (http://www.datamonkey.org/).
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Cites
Gelman, A., Carlin, J. B., Stern, H. S., & Rubin, D. B. (2003) · doi:10.1201/9780429258480 · Cited by 27,276
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Detecting Individual Sites Subject to Episodic Diversifying Selection
Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811
Self-citationAntibody Recognition of a Highly Conserved Influenza Virus Epitope
Ekiert, D. C., Bhabha, G., Elsliger, M.-A., Friesen, R. H. E., Jongeneelen, M., Throsby, M., Goudsmit, J., & Wilson, I. A. (2009) · Science · doi:10.1126/science.1171491 · Cited by 1,326
Corti, D., Voss, J., Gamblin, S. J., Codoni, G., Macagno, A., Jarrossay, D., Vachieri, S. G., Pinna, D., Minola, A., Vanzetta, F., et al. (2011) · Science · doi:10.1126/science.1205669 · Cited by 1,203
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9
McLellan, J. S., Pancera, M., Carrico, C., Gorman, J., Julien, J.-P., Khayat, R., Louder, R., Pejchal, R., Sastry, M., Dai, K., et al. (2011) · Nature · doi:10.1038/nature10696 · Cited by 830
A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield
Pejchal, R., Doores, K. J., Walker, L. M., Khayat, R., Huang, P.-S., Wang, S.-K., Stanfield, R. L., Julien, J.-P., Ramos, A., Crispin, M., et al. (2011) · Science · doi:10.1126/science.1213256 · Cited by 694
A random effects branch-site model for detecting episodic diversifying selection
Kosakovsky Pond, S. L., Murrell, B., Fourment, M., Frost, S. D. W., Delport, W., & Scheffler, K. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr125 · Cited by 400
Self-citationCorrecting the Bias of Empirical Frequency Parameter Estimators in Codon Models
Kosakovsky Pond, S., Delport, W., Muse, S. V., & Scheffler, K. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011230 · Cited by 51
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Cited by
Martin, D. P., Weaver, S., Tegally, H., San, E. J., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., et al. (2021) · doi:10.1101/2021.02.23.21252268 · Cited by 291
“Until SARS-CoV-2 emerged in 2019, analyses of natural selection using a few thousand viral sequences would be considered “large scale” (Murrell et al., 2013).”
Self-citationFerrareze, P. A. G., Franceschi, V. B., Mayer, A. D. M., Caldana, G. D., Zimerman, R. A., & Thompson, C. E. (2021) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2021.104941 · Cited by 82
A conserved fertilization complex bridges sperm and egg in vertebrates
Deneke, V. E., Blaha, A., Lu, Y., Suwita, J. P., Draper, J. M., Phan, C. S., Panser, K., Schleiffer, A., Jacob, L., Humer, T., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.035 · Cited by 78
Wheeler, L. C., Walker, J. F., Ng, J., Deanna, R., Dunbar-Wallis, A., Backes, A., Pezzi, P. H., Palchetti, M. V., Robertson, H. M., Monaghan, A., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac044 · Cited by 63
Understanding the evolution of immune genes in jawed vertebrates
Vinkler, M., Fiddaman, S. R., Těšický, M., O'Connor, E. A., Savage, A. E., Lenz, T. L., Smith, A. L., Kaufman, J., Bolnick, D. I., Davies, C. S., et al. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14181 · Cited by 55
Metadata
- Authors
- Murrell, B., Moola, S., Mabona, A., Weighill, T., Sheward, D., Kosakovsky Pond, S. L., & Scheffler, K.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-02-18
- Volume
- 30
- Issue
- 5
- Pages
- 1196-1205
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2108512869
- Cited by
- 1,358
- References
- 10
- FWCI
- 43.50
- Type
- journal article
- Language
- en
- Open access
- bronze
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