Modeling sequence evolution in acute HIV-1 infection (Q37384535)

20 August 2017

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title

Modeling sequence evolution in acute HIV-1 infection (English)

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Corrigendum to “Modeling sequence evolution in acute HIV-1 infection” [J. Theor. Biol. 261 (2009) 341–360]

20 August 2017

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corrigendum / erratum

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20 August 2017

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20 August 2017

Tanmoy Bhattacharya

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Beatrice H Hahn

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Jesus F Salazar-Gonzalez

object named as

Jesus F Salazar-Gonzalez

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Michael P Busch

1 reference

20 August 2017

George M Shaw

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20 August 2017

Brandon F Keele

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20 August 2017

Alan S Perelson

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20 August 2017

Michael S Saag

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20 August 2017

Brian Gaschen

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20 August 2017

Paul A Goepfert

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Ha Youn Lee

1 reference

20 August 2017

Elena E Giorgi

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20 August 2017

Gayathri S Athreya

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20 August 2017

Kimmy T Pham

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20 August 2017

J Michael Kilby

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20 August 2017

language of work or name

English

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publication date

4 August 2009

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Journal of Theoretical Biology

20 August 2017

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inferred from page(s)

published in

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20 August 2017

261

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20 August 2017

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20 August 2017

341-360

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maintained by WikiProject

20 August 2017

WikiProject Mathematics

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cites work

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Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1.

6 September 2017

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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

6 September 2017

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

6 September 2017

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

6 September 2017

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Determination of virus burst size in vivo using a single-cycle SIV in rhesus macaques

6 September 2017

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6 September 2017

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Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1

6 September 2017

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Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity

6 September 2017

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Role of maternal autologous neutralizing antibody in selective perinatal transmission of human immunodeficiency virus type 1 escape variants

6 September 2017

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Relaxed phylogenetics and dating with confidence

6 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.

6 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Comparing likelihood and Bayesian coalescent estimation of population parameters

6 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Natural variation in Vif: differential impact on APOBEC3G/3F and a potential role in HIV-1 diversification

6 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Genome sequencing in microfabricated high-density picolitre reactors

6 September 2017

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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

6 September 2017

1 reference

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Bayesian coalescent inference of past population dynamics from molecular sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

A new cell-based assay for measuring the forward mutation rate of HIV-1.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Retroviral restriction by APOBEC proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Human immunodeficiency virus type 1 (HIV-1) diversity at time of infection is not restricted to certain risk groups or specific HIV-1 subtypes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Envelope variants from women recently infected with clade A human immunodeficiency virus type 1 confer distinct phenotypes that are discerned by competition and neutralization experiments.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Antibody neutralization and escape by HIV-1

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Timing the ancestor of the HIV-1 pandemic strains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Viral dynamics of acute HIV-1 infection

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Sexual transmission of HIV: infectiousness and prevention

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Maximum likelihood estimation of population growth rates based on the coalescent

6 September 2017

1 reference

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Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Clinical picture of primary HIV infection presenting as a glandular-fever-like illness

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Mapping trait loci by use of inferred ancestral recombination graphs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Forward mutation rate of human immunodeficiency virus type 1 in a T lymphoid cell line

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Modeling plasma virus concentration during primary HIV infection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Gene genealogy in a population of variable size

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

High titers of cytopathic virus in plasma of patients with symptomatic primary HIV-1 infection

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Inheritance of defective extremities

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Intermittent low-level viremia in very early primary HIV-1 infection.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Two-sample tests for comparing intra-individual genetic sequence diversity between populations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

A robust measure of HIV-1 population turnover within chronically infected individuals.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

HIV type 1 variants transmitted to women in Kenya require the CCR5 coreceptor for entry, regardless of the genetic complexity of the infecting virus

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

A stochastic modeling of early HIV-1 population dynamics.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Viral dynamics in primary HIV-1 infection. Karolinska Institutet Primary HIV Infection Study Group.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

A stochastic model for primary HIV infection: optimal timing of therapy.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

A stochastic model for early HIV-1 population dynamics.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Stochastic modeling of the dynamics of CD4+ T-cell infection by HIV and some Monte Carlo studies.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760689

Monte Carlo estimates of natural variation in HIV infection

2 September 2018

1 reference

12 December 2020

Estimating the pattern of nucleotide substitution

1 reference

12 December 2020

Clinical and epidemiologic features of primary HIV infection

1 reference

12 December 2020

Diagnosis of primary HIV-1 infection and duration of follow-up after HIV exposure. Karolinska Institute Primary HIV Infection Study Group

1 reference

12 December 2020

10.1016/J.JTBI.2009.07.038

Identifiers

DOI

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

19660475

1 reference