An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data (Q30781299)

6 November 2017

An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data (English)

1 reference

6 November 2017

0 references

1 reference

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Art Poon

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

author name string

Rosemary M McCloskey

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Richard H Liang

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

P Richard Harrigan

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

language of work or name

1 reference

19 March 2014

1 reference

6 November 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

volume

88

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

page(s)

6181-6194

1 reference

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describes a project that uses

10 June 2020

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=4093844

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Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions

20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

20 June 2018

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The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

20 June 2018

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Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants

20 June 2018

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Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1

20 June 2018

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Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

20 June 2018

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Reconstruction and Function of Ancestral Center-of-Tree Human Immunodeficiency Virus Type 1 Proteins

20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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Human Immunodeficiency Virus Type 1 Subtype B Ancestral Envelope Protein Is Functional and Elicits Neutralizing Antibodies in Rabbits Similar to Those Elicited by a Circulating Subtype B Envelope

20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

1 reference

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Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy

20 June 2018

1 reference

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Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis

20 June 2018

1 reference

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HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Genotypic and phenotypic characterization of HIV-1 patients with primary infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Application and accuracy of molecular phylogenies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Rapid evolution of RNA genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Molecules as documents of evolutionary history

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Generation of hybrid human immunodeficiency virus by homologous recombination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Amino acid substitution matrices from protein blocks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Associations between substance use, erectile dysfunction medication and recent HIV infection among men who have sex with men.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Empirical and hierarchical Bayesian estimation of ancestral states.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Inferring the root of a phylogenetic tree

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Experimental Phylogenetics: Generation of a Known Phylogeny

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4093844

Recombination and the molecular clock

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24648453

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Comparison of clinical features of acute HIV-1 infection in patients infected sexually or through injection drug use. The Investigators of the Québec Primary HIV Infection Study

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24648453

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/JVI.00483-14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

PubMed publication ID

24648453

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24648453%20AND%20SRC:MED&resulttype=core&format=json