Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses (Q33549119)

28 July 2017

title

Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses (English)

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28 July 2017

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28 July 2017

5

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28 July 2017

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Andrew Rambaut

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Cadhla Firth

object named as

Cadhla Firth

series ordinal

1

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Marc A. Suchard

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4

object named as

Marc A Suchard

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28 July 2017

Andrew Kitchen

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28 July 2017

publication date

2 April 2010

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Molecular Biology and Evolution

28 July 2017

published in

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28 July 2017

volume

27

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28 July 2017

issue

9

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28 July 2017

page(s)

2038-2051

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How long ago did smallpox virus emerge?

28 July 2017

cites work

1 reference

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The evolutionary biology of poxviruses

21 June 2018

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Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2

21 June 2018

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Bayesian phylogeography finds its roots

21 June 2018

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Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

21 June 2018

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Dating the emergence of pandemic influenza viruses

21 June 2018

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Isolation and characterization of adenoviruses persistently shed from the gastrointestinal tract of non-human primates

21 June 2018

1 reference

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Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses

21 June 2018

1 reference

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Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97.

21 June 2018

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Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence

21 June 2018

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The genomic and epidemiological dynamics of human influenza A virus

21 June 2018

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Bayesian coalescent analysis reveals a high rate of molecular evolution in GB virus C

21 June 2018

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Rates of evolutionary change in viruses: patterns and determinants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

The effect of inappropriate calibration: three case studies in molecular ecology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

BEAST: Bayesian evolutionary analysis by sampling trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

On the origin of smallpox: correlating variola phylogenics with historical smallpox records

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

The evolutionary genetics of viral emergence

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

21 June 2018

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Elevated substitution rates estimated from ancient DNA sequences

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Evidence for time dependency of molecular rate estimates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Out of Africa: a molecular perspective on the introduction of yellow fever virus into the Americas

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Ancient papillomavirus-host co-speciation in Felidae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Temporal trends in gonococcal population genetics in a high prevalence urban community

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

JC virus evolution and its association with human populations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Evolution of BK virus based on complete genome data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Genome sequence diversity and clues to the evolution of variola (smallpox) virus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Comparing phylogenetic codivergence between polyomaviruses and their hosts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Relaxed phylogenetics and dating with confidence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Molecular clocks: when times are a-changin'

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Genome variation of human papillomavirus types: phylogenetic and medical implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Phylogenetic analysis of the main neutralization and hemagglutination determinants of all human adenovirus prototypes as a basis for molecular classification and taxonomy.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

On the mutation rate of herpes simplex virus type 1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Bayesian coalescent inference of past population dynamics from molecular sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

High rate of viral evolution associated with the emergence of carnivore parvovirus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

HyPhy: hypothesis testing using phylogenies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

The phylogeography of human viruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Poxvirus genomes: a phylogenetic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Inference of viral evolutionary rates from molecular sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Extensive gene gain associated with adaptive evolution of poxviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Molecular Evolution of Adenoviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Mutation spectra of herpes simplex virus type 1 thymidine kinase mutants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Phylogenetic analysis of varicella-zoster virus: evidence of intercontinental spread of genotypes and recombination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Exploring the demographic history of DNA sequences using the generalized skyline plot

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Bayesian selection of continuous-time Markov chain evolutionary models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Toward a comprehensive phylogeny for mammalian and avian herpesviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Evolutionary diversification of protein-coding genes of hantaviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

An integrated framework for the inference of viral population history from reconstructed genealogies.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Acute and persistent viral life strategies and their relationship to emerging diseases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Simian immunodeficiency virus (SIV) from sun-tailed monkeys (Cercopithecus solatus): evidence for host-dependent evolution of SIV within the C. lhoesti superspecies.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

MODELTEST: testing the model of DNA substitution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Rates of spontaneous mutation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Mutation rate of GB virus C/hepatitis G virus over the entire genome and in subgenomic regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Evolution of human papillomavirus type 18: an ancient phylogenetic root in Africa and intratype diversity reflect coevolution with human ethnic groups

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Molecular phylogeny of the alphaherpesvirinae subfamily and a proposed evolutionary timescale

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Coevolution of papillomaviruses with human populations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

A constant rate of spontaneous mutation in DNA-based microbes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Phylogenetic analysis of GB viruses A and C: evidence for cospeciation between virus isolates and their primate hosts

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

The effect of paralogous lineages on the application of reconciliation analysis by cophylogeny mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Macroevolution of complex retroviruses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Evolution of four BK virus subtypes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

RDP2: recombination detection and analysis from sequence alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Evolution of Human Polyomavirus JC: Implications for the Population History of Humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Relationships between BK virus lineages and human populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ088

Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Severe acute respiratory syndrome

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

The out of Africa model of varicella-zoster virus evolution: single nucleotide polymorphisms and private alleles distinguish Asian clades from European/North American clades

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Evolution of Picornaviridae: An examination of phylogenetic relationships and cophylogeny

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107591

Relativity for molecular clocks

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20363828

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Evolutionary changes of nucleotide sequences of papova viruses BKV and SV40: They are possibly hybrids

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20363828

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSQ088

1 reference

28 July 2017

1 reference

28 July 2017

1 reference