Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection (Q30469621)

10 August 2017

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection (English)

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10 August 2017

whole genome sequencing

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10

Sante Gnerre

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Olivier Gasser

Olivier Gasser

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Chanson J Brumme

Chanson J Brumme

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Zabrina L Brumme

Zabrina L Brumme

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Christian Brander

Christian Brander

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Huldrych F Günthard

Huldrych F Günthard

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Damien C Tully

Damien Tully

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Bruce D. Walker

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Bruce D Walker

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Florencia Pereyra

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Marcus Altfeld

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Hendrik Streeck

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Eric Rosenberg

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Todd M Allen

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Suzane Bazner

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Jenna Rychert

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Karen A Power

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Adrianne Gladden-Young

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Adrianne D Gladden

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Jake P Tinsley

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Yaoyu Wang

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Karen L Axten

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Patrick Charlebois

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Christine M Malboeuf

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Rachel L Erlich

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Lisa M Green

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Andrew Berical

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Ruchi Newman

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Bruce W Birren

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Matthew R Henn

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Christian L Boutwell

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Niall J Lennon

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Alexander R Macalalad

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Aaron M Berlin

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Elizabeth M Ryan

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Michael C Zody

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Monica Casali

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Allyson K Bloom

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Tim Dudek

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Laura Battis

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Michael Kemper

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Qiandong Zeng

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Terrance P Shea

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Sharvari Gujja

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Carmen Zedlack

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Christoph Hess

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Ken H Mayer

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Joshua Z Levin

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Sarah K Young

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Heiko Jessen

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10 August 2017

language of work or name

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8 March 2012

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10 August 2017

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e1002529

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Creative Commons Attribution 4.0 International

10 August 2017

start time

8 March 2012

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

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Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

20 June 2018

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Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection

20 June 2018

1 reference

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Dynamics of viral evolution and CTL responses in HIV-1 infection

20 June 2018

1 reference

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Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

20 June 2018

1 reference

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Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing

20 June 2018

1 reference

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Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Mathematical modeling of ultradeep sequencing data reveals that acute CD8 T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Mosaic vaccines elicit CD8 T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys

20 June 2018

1 reference

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Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

20 June 2018

1 reference

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HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins

20 June 2018

1 reference

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Ultradeep pyrosequencing detects complex patterns of CD8 T-lymphocyte escape in simian immunodeficiency virus-infected macaques

20 June 2018

1 reference

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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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Human immunodeficiency virus type 1-specific CD8 T-cell responses during primary infection are major determinants of the viral set point and loss of CD4 T cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Adaptation of HIV-1 to human leukocyte antigen class I

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Immune-driven recombination and loss of control after HIV superinfection.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 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=3297584

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid

20 June 2018

1 reference

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

20 June 2018

1 reference

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Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Cross-clade detection of HIV-1-specific cytotoxic T lymphocytes does not reflect cross-clade antiviral activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Selection on the human immunodeficiency virus type 1 proteome following 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=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

De novo generation of escape variant-specific CD8 T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 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=3297584

Genome sequencing in microfabricated high-density picolitre reactors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

CD8 Epitope Escape and Reversion in Acute HCV 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=3297584

Consequences of cytotoxic T-lymphocyte escape: common escape mutations in simian immunodeficiency virus are poorly recognized in naive hosts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 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=3297584

Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV 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=3297584

Rapid evolution of the neutralizing antibody response to HIV type 1 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=3297584

An SNP map of the human genome generated by reduced representation shotgun sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Development of a malaria vaccine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during 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=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Prognosis in HIV-1 infection predicted by the quantity of virus in plasma

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Homologous recombination promoted by reverse transcriptase during copying of two distinct RNA templates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Quantifying the uncertainty in forecasts of anthropogenic climate change

20 June 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

Precise identification of a human immunodeficiency virus type 1 antigen processing mutant

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

HIV-1 viral escape in infancy followed by emergence of a variant-specific CTL response.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

Reducing chimera formation during PCR amplification to ensure accurate genotyping.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PPAT.1002529

Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22412369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

HIV-1 Epitope-Specific CD8 T Cell Responses Strongly Associated with Delayed Disease Progression Cross-Recognize Epitope Variants Efficiently

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22412369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PPAT.1002529

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

22412369

1 reference