(Q24538985)

Sergei L. Kosakovsky Pond

10

object named as

Christos J Petropoulos

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4

object named as

Sergei L Kosakovsky Pond

0 references

Susan J Little

11

object named as

Susan J Little

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author name string

Simon D W Frost

1

0 references

Terri Wrin

2

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Davey M Smith

3

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Yang Liu

5

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Ellen Paxinos

6

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Colombe Chappey

7

0 references

Justin Galovich

8

0 references

Jeff Beauchaine

9

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Douglas D Richman

Proceedings of the National Academy of Sciences of the United States of America

12

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language of work or name

English

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publication date

20 December 2005

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published in

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volume

102

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issue

51

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page(s)

18514-9

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cites work

Codon-substitution models for heterogeneous selection pressure at amino acid sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Identification of common molecular subsequences

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Timing the ancestor of the HIV-1 pandemic strains

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

The impact of the syncytium-inducing phenotype of human immunodeficiency virus on disease progression

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

HyPhy: hypothesis testing using phylogenies

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Antibody neutralization and escape by HIV-1

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Viral dynamics in human immunodeficiency virus type 1 infection

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Decay characteristics of HIV-1-infected compartments during combination therapy

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Correlation between env V1/V2 region diversification and neutralizing antibodies during primary infection by simian immunodeficiency virus sm in rhesus macaques

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Comprehensive analysis of human immunodeficiency virus type 1 (HIV-1)-specific gamma interferon-secreting CD8+ T cells in primary HIV-1 infection

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Association between virus-specific T-cell responses and plasma viral load in human immunodeficiency virus type 1 subtype C infection

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Virus population homogenization following acute human immunodeficiency virus type 1 infection

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Role of N-linked glycans in a human immunodeficiency virus envelope glycoprotein: effects on protein function and the neutralizing antibody response

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Neutralizing antibodies have limited effects on the control of established HIV-1 infection in vivo.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

The amino acid following an asn-X-Ser/Thr sequon is an important determinant of N-linked core glycosylation efficiency

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Changes in the extracellular envelope glycoprotein of variants that evolve during the course of simian immunodeficiency virus SIVMne infection affect neutralizing antibody recognition, syncytium formation, and macrophage tropism but not replication,

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Specific N-linked and O-linked glycosylation modifications in the envelope V1 domain of simian immunodeficiency virus variants that evolve in the host alter recognition by neutralizing antibodies

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Regulation of N-linked core glycosylation: use of a site-directed mutagenesis approach to identify Asn-Xaa-Ser/Thr sequons that are poor oligosaccharide acceptors

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Evolutionary pattern of intra-host pathogen antigenic drift: effect of cross-reactivity in immune response

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Evolution of the V3 envelope domain in proviral sequences and isolates of human immunodeficiency virus type 1 during transition of the viral biological phenotype

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Analysis of the V3 loop in neutralization-resistant human immunodeficiency virus type 1 variants by direct solid-phase DNA sequencing

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

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

30 May 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Envelope diversity, coreceptor usage and syncytium-inducing phenotype of HIV-1 variants in saliva and blood during primary infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapy

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

A new perspective on V3 phenotype prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Linkage of amino acid variation and evolution of human immunodeficiency virus type 1 gp120 envelope glycoprotein (subtype B) with usage of the second receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

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/10.1073%2FPNAS.0504658102

Expression of hemagglutinin protein of rinderpest virus in transgenic tobacco and immunogenicity of plant-derived protein in a mouse model

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Functional mixed effects models

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

The study of long-term HIV dynamics using semi-parametric non-linear mixed-effects models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

A simple hierarchical approach to modeling distributions of substitution rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

A regression modeling approach for describing patterns of HIV genetic variation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Neutralizing Antibody Responses to Human Immunodeficiency Virus Type 1 in Primary Infection and Long‐Term‐Nonprogressive Infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

Development of the antibody response in acute HIV-1 infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0504658102

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/10.1073%2FPNAS.0504658102

A longitudinal assessment of autologous neutralizing antibodies in children perinatally infected with human immunodeficiency virus type 1.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310509

Kinetics of appearance of neutralizing antibodies in 12 patients with primary or recent HIV-1 infection and relationship with plasma and cellular viral loads

29 November 2018

1 reference

PubMed

12 December 2020

1 reference

12 December 2020

Detecting hypermutations in viral sequences with an emphasis on G --> A hypermutation

1 reference

PubMed

12 December 2020

Course of Specific T Lymphocyte Cytotoxicity, Plasma and Cellular Viral Loads, and Neutralizing Antibody Titers in 17 Recently Seroconverted HIV Type 1-Infected Patients

1 reference

PubMed

12 December 2020

Identifiers

DOI

10.1073/PNAS.0504658102

1 reference

release_gvwiz6qlkbbjnbp2s32fi2ahlu

0 references

0 references

3509231

1 reference

1 reference

3509231

PubMed publication ID

16339909

1 reference