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BEAST: Bayesian evolutionary analysis by sampling trees.
Drummond AJ, Rambaut A. Drummond AJ, et al. BMC Evol Biol. 2007 Nov 8;7:214. doi: 10.1186/1471-2148-7-214. BMC Evol Biol. 2007. PMID: 17996036 Free PMC article.
Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. ...CONCLUSION: BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provid …
Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary …
Canalization of the evolutionary trajectory of the human influenza virus.
Bedford T, Rambaut A, Pascual M. Bedford T, et al. BMC Biol. 2012 Apr 30;10:38. doi: 10.1186/1741-7007-10-38. BMC Biol. 2012. PMID: 22546494 Free PMC article.
We implement this model in a large-scale individual-based simulation, and in doing so, we find a remarkable correspondence between model behavior and observed influenza dynamics. ...In the model, the influenza population shows a 1- to 2-year timescale of repe …
We implement this model in a large-scale individual-based simulation, and in doing so, we find a remarkable correspondence bet …
BEAST 2: a software platform for Bayesian evolutionary analysis.
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. Bouckaert R, et al. PLoS Comput Biol. 2014 Apr 10;10(4):e1003537. doi: 10.1371/journal.pcbi.1003537. eCollection 2014 Apr. PLoS Comput Biol. 2014. PMID: 24722319 Free PMC article.
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 sof …
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This softw …
The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach.
Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL. Archer J, et al. PLoS Comput Biol. 2010 Dec 16;6(12):e1001022. doi: 10.1371/journal.pcbi.1001022. PLoS Comput Biol. 2010. PMID: 21187908 Free PMC article.
Here we demonstrate our software by analyzing two temporally sampled HIV-1 intra-patient datasets from a clinical study of maraviroc. ...The objective is to determine viral tropism (CCR5 versus CXCR4 usage) and track the evolution of minority CXCR4-using variants that may …
Here we demonstrate our software by analyzing two temporally sampled HIV-1 intra-patient datasets from a clinical study of maraviroc. …
The molecular population genetics of HIV-1 group O.
Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, Worobey M, Vandamme AM. Lemey P, et al. Genetics. 2004 Jul;167(3):1059-68. doi: 10.1534/genetics.104.026666. Genetics. 2004. PMID: 15280223 Free PMC article.
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. ...Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar …
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low pr …
Inferring confidence sets of possibly misspecified gene trees.
Strimmer K, Rambaut A. Strimmer K, et al. Proc Biol Sci. 2002 Jan 22;269(1487):137-42. doi: 10.1098/rspb.2001.1862. Proc Biol Sci. 2002. PMID: 11798428 Free PMC article.
Here, three methods to infer confidence sets that are robust against model misspecification are compared, including a new approach based on estimating the confidence in a specific tree using expected-likelihood weights. ...
Here, three methods to infer confidence sets that are robust against model misspecification are compared, including a new approach ba …
HIV evolutionary dynamics within and among hosts.
Lemey P, Rambaut A, Pybus OG. Lemey P, et al. AIDS Rev. 2006 Jul-Sep;8(3):125-40. AIDS Rev. 2006. PMID: 17078483 Review.
The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of statistical models and inference techniques have been developed to reconstruct the HIV evolutionary history and to investigate the population gen …
The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of stati …
Evolutionary rate differences in trypanosomes.
Stevens J, Rambaut A. Stevens J, et al. Infect Genet Evol. 2001 Dec;1(2):143-50. doi: 10.1016/s1567-1348(01)00018-1. Infect Genet Evol. 2001. PMID: 12798029
While early 18S rRNA-based studies were hampered by highly variable substitution rates and long-branch attraction, it is apparent that genuine differences in evolution rates within localized clades do exist and questions remain regarding what rate or rates such clades are evolvin …
While early 18S rRNA-based studies were hampered by highly variable substitution rates and long-branch attraction, it is apparent that genui …
The power of relative rates tests depends on the data.
Bromham L, Penny D, Rambaut A, Hendy MD. Bromham L, et al. J Mol Evol. 2000 Mar;50(3):296-301. doi: 10.1007/s002399910034. J Mol Evol. 2000. PMID: 10754073
Many molecular dating studies use a "clock test" to identify and exclude sequences that vary in rate between lineages. However, these clock tests should not be relied upon without a critical examination of their effectiveness at removing rate variable sequences from …
Many molecular dating studies use a "clock test" to identify and exclude sequences that vary in rate between lineages. However, these …
The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach.
Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A. Pybus OG, et al. Mol Biol Evol. 2003 Mar;20(3):381-7. doi: 10.1093/molbev/msg043. Mol Biol Evol. 2003. PMID: 12644558
Hepatitis C virus (HCV) is a leading cause of liver cancer and cirrhosis, and Egypt has possibly the highest HCV prevalence worldwide. ...Because our results are consistent with a demographic scenario specified a priori, they also provide an objective test of …
Hepatitis C virus (HCV) is a leading cause of liver cancer and cirrhosis, and Egypt has possibly the highest HCV prevalence worldwide …
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