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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 …
Phylogenetic evidence for recombination in dengue virus.
Holmes EC, Worobey M, Rambaut A. Holmes EC, et al. Mol Biol Evol. 1999 Mar;16(3):405-9. doi: 10.1093/oxfordjournals.molbev.a026121. Mol Biol Evol. 1999. PMID: 10331266
A split decomposition analysis of dengue (DEN) virus gene sequences revealed extensive networked evolution, indicative of recombination, among DEN-1 strains but not within serotypes DEN-2, DEN-3, or DEN-4. ...To map the breakpoints and test their statistical support, we de
A split decomposition analysis of dengue (DEN) virus gene sequences revealed extensive networked evolution, indicative of recombinati
Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.
Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Jenkins GM, et al. J Mol Evol. 2002 Feb;54(2):156-65. doi: 10.1007/s00239-001-0064-3. J Mol Evol. 2002. PMID: 11821909
Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensi …
Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihoo …
Inferring the rate and time-scale of dengue virus evolution.
Twiddy SS, Holmes EC, Rambaut A. Twiddy SS, et al. Mol Biol Evol. 2003 Jan;20(1):122-9. doi: 10.1093/molbev/msg010. Mol Biol Evol. 2003. PMID: 12519914
To understand the rate at which genetic diversification occurs in dengue virus and to infer the time-scale of its evolution, we employed a maximum likelihood method that uses information about times of virus sampling to estimate the rate of molecular evolution in a
To understand the rate at which genetic diversification occurs in dengue virus and to infer the time-scale of its evolution, we employed …
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 …
Inference of viral evolutionary rates from molecular sequences.
Drummond A, Pybus OG, Rambaut A. Drummond A, et al. Adv Parasitol. 2003;54:331-58. doi: 10.1016/s0065-308x(03)54008-8. Adv Parasitol. 2003. PMID: 14711090 Review.
The evolutionary dynamics of endogenous retroviruses.
Katzourakis A, Rambaut A, Pybus OG. Katzourakis A, et al. Trends Microbiol. 2005 Oct;13(10):463-8. doi: 10.1016/j.tim.2005.08.004. Trends Microbiol. 2005. PMID: 16109487
We present a model that unifies current knowledge of ERV biology into a single evolutionary framework. The model predicts the possible long-term outcomes of retroviral germline infection and can account for the variable patterns of observed ERV genetic diversity. We …
We present a model that unifies current knowledge of ERV biology into a single evolutionary framework. The model predicts the …
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.
Shapiro B, Rambaut A, Pybus OG, Holmes EC. Shapiro B, et al. Mol Biol Evol. 2006 Sep;23(9):1724-30. doi: 10.1093/molbev/msl037. Epub 2006 Jun 14. Mol Biol Evol. 2006. PMID: 16774976
To investigate the pervasiveness of epistasis in RNA viruses, we used a parsimony-based computational method to identify pairs of co-occurring mutations along phylogenies of 177 RNA virus genes. ...
To investigate the pervasiveness of epistasis in RNA viruses, we used a parsimony-based computational method to identify pairs of co- …
JC virus evolution and its association with human populations.
Shackelton LA, Rambaut A, Pybus OG, Holmes EC. Shackelton LA, et al. J Virol. 2006 Oct;80(20):9928-33. doi: 10.1128/JVI.00441-06. J Virol. 2006. PMID: 17005670 Free PMC article.
The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and it is often transmitted from parents to children. ...Because of its presumed codivergence with humans, JCV has been used as a genetic …
The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and i …
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 …
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