(Q33394563)

26 July 2017

Frequent toggling between alternative amino acids is driven by selection in HIV-1 (English)

1 reference

26 July 2017

Konrad Scheffler

2

0 references

author name string

Wayne Delport

series ordinal

1

1 reference

PubMed ID

19096508

26 July 2017

Cathal Seoighe

series ordinal

3

1 reference

26 July 2017

19 December 2008

1 reference

26 July 2017

1 reference

26 July 2017

4

1 reference

26 July 2017

e1000242

1 reference

26 July 2017

12

1 reference

Creative Commons Attribution 4.0 International

26 July 2017

start time

19 December 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection

14 July 2018

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Central role of reverting mutations in HLA associations with human immunodeficiency virus set point

14 July 2018

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Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage

14 July 2018

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HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24.

14 July 2018

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Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication

14 July 2018

1 reference

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Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A.

14 July 2018

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Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1

14 July 2018

1 reference

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Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection

14 July 2018

1 reference

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Recognition of a defined region within p24 gag by CD8+ T cells during primary human immunodeficiency virus type 1 infection in individuals expressing protective HLA class I alleles

14 July 2018

1 reference

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Exploiting the defensive sugars of HIV-1 for drug and vaccine design

14 July 2018

1 reference

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Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

14 July 2018

1 reference

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Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution

14 July 2018

1 reference

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Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites

14 July 2018

1 reference

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HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8(+) T Cell Response against HIV-1.

14 July 2018

1 reference

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Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution

14 July 2018

1 reference

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The role of compensatory mutations in the emergence of drug resistance

14 July 2018

1 reference

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Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection.

14 July 2018

1 reference

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Robust inference of positive selection from recombining coding sequences

14 July 2018

1 reference

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Adaptation to different human populations by HIV-1 revealed by codon-based analyses

14 July 2018

1 reference

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Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1

14 July 2018

1 reference

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Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection

14 July 2018

1 reference

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Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Reversion in vivo after inoculation of a molecular proviral DNA clone of simian immunodeficiency virus with a cytotoxic-T-lymphocyte escape mutation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA.

14 July 2018

1 reference

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Not so different after all: a comparison of methods for detecting amino acid sites under selection

14 July 2018

1 reference

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HyPhy: hypothesis testing using phylogenies

14 July 2018

1 reference

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Estimating the frequency of events that cause multiple-nucleotide changes

14 July 2018

1 reference

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HIV and SIV CTL escape: implications for vaccine design

14 July 2018

1 reference

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Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Mapping the antigenic and genetic evolution of influenza virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection

14 July 2018

1 reference

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WebLogo: A Sequence Logo Generator

14 July 2018

1 reference

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Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

The causes and consequences of HIV evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Population dynamics of rapid fixation in cytotoxic T lymphocyte escape mutants of influenza A

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Antibody domain exchange is an immunological solution to carbohydrate cluster recognition

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Antibody neutralization and escape by HIV-1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Rapid evolution of the neutralizing antibody response to HIV type 1 infection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

The influence of HLA genotype on AIDS

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Magnitude of functional CD8+ T-cell responses to the gag protein of human immunodeficiency virus type 1 correlates inversely with viral load in plasma

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Genealogical evidence for positive selection in the nef gene of HIV-1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Specific proteolytic cleavages limit the diversity of the pool of peptides available to MHC class I molecules in living cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

A codon-based model of nucleotide substitution for protein-coding DNA sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

Evolutionary trees from DNA sequences: A maximum likelihood approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2592544

HIV evolution: CTL escape mutation and reversion after transmission.

14 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

CD8+ T-cell responses to different HIV proteins have discordant associations with viral load

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Reversion of CTL escape–variant immunodeficiency viruses in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

GARD: a genetic algorithm for recombination detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

CD4+ T cell kinetics and activation in human immunodeficiency virus-infected patients who remain viremic despite long-term treatment with protease inhibitor-based therapy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

A model of directional selection applied to the evolution of drug resistance in HIV-1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Hitting HIV where it hurts: an alternative approach to HIV vaccine design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Potential impact of recombination on sitewise approaches for detecting positive natural selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000242

Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19096508

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A longitudinal study of neutralizing antibodies and disease progression in HIV-1-infected subjects

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19096508

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PPAT.1000242

1 reference

26 July 2017

1 reference

26 July 2017

1 reference

PubMed ID

19096508