Lista de obras - John Coffin - Dominio Público Uruguay

A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses

artículo científico publicado en 2014

A9 A method to obtain full-length HIV proviral sequences and their sites of integration

ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia

artículo científico publicado en 2007

Amplifying and quantifying HIV-1 RNA in HIV infected individuals with viral loads below the limit of detection by standard clinical assays

artículo científico publicado en 2011

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

artículo científico publicado en 2013

Antiretroviral intensification and valproic acid lack sustained effect on residual HIV-1 viremia or resting CD4+ cell infection

artículo científico publicado en 2010

Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class

artículo científico publicado en 2013

Characterization of hortulanus endogenous murine leukemia virus, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup

artículo científico publicado en 2005

Characterization, mapping, and distribution of the two XMRV parental proviruses

artículo científico publicado en 2012

Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans

scientific article published on 10 July 2019

Clonal sequences recovered from plasma from patients with residual HIV-1 viremia and on intensified antiretroviral therapy are identical to replicating viral RNAs recovered from circulating resting CD4+ T cells

artículo científico publicado en 2011

Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo

artículo científico publicado en 2016

Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors

artículo científico publicado en 2019

Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences

artículo científico publicado en 2010

Correction: The Effect of Raltegravir Intensification on Low-level Residual Viremia in HIV-Infected Patients on Antiretroviral Therapy: A Randomized Controlled Trial.

artículo científico publicado en 2011

Depletion of latent HIV-1 infection in vivo: a proof-of-concept study

artículo científico publicado en 2005

Early Emergence and Long-Term Persistence of HIV-Infected T-Cell Clones in Children

artículo científico publicado en 2021

Endogenous non-retroviral RNA virus elements in mammalian genomes

artículo científico publicado en 2010

Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

artículo científico publicado en 2011

Evaluation of the pathogenesis of decreasing CD4(+) T cell counts in human immunodeficiency virus type 1-infected patients receiving successfully suppressive antiretroviral therapy

artículo científico publicado en 2009

Failure to confirm XMRV/MLVs in the blood of patients with chronic fatigue syndrome: a multi-laboratory study

artículo científico publicado en 2011

Flexible use of nuclear import pathways by HIV-1.

artículo científico publicado en 2010

Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase

artículo científico publicado en 2008

Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy

artículo científico publicado en 2010

HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus

scientific article published on 01 October 2019

HIV Pathogenesis: Dynamics and Genetics of Viral Populations and Infected Cells ⬇️

artículo científico publicado el 1 de enero de 2013

HIV-1 continues to replicate and evolve in patients with natural control of HIV infection

artículo científico publicado en 2010

HIV-1 expression within resting CD4+ T cells after multiple doses of vorinostat

artículo científico publicado en 2014

HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy

artículo científico publicado en 2019

HIV-1 infection leads to increased transcription of human endogenous retrovirus HERV-K (HML-2) proviruses in vivo but not to increased virion production

artículo científico publicado en 2014

Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection

artículo científico publicado en 2012

Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy

artículo científico publicado en 2014

Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance

artículo científico publicado en 2009

Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients

artículo científico publicado en 2010

Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy

artículo científico publicado en 2008

Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults

artículo científico publicado en 2018

Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control

scientific article published on 08 December 2008

Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule

artículo científico publicado en 2011

Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision

artículo científico publicado en 2005

Mouse DNA contamination in human tissue tested for XMRV

artículo científico publicado en 2010

Multi-site adaptation in the presence of infrequent recombination

artículo científico publicado en 2010

Multiple sources of contamination in samples from patients reported to have XMRV infection

artículo científico publicado en 2012

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

artículo científico publicado en 2005

Mutations in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine resistance

artículo científico publicado en 2006

New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma

artículo científico publicado en 2003

No evidence of HIV replication in children on antiretroviral therapy.

artículo científico publicado en 2017

Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways

artículo científico publicado en 2004

Ongoing HIV Replication During ART Reconsidered

article

Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy

artículo científico publicado en 2015

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data

artículo científico publicado en 2014

Patterns of Human Immunodeficiency Virus type 1 recombination ex vivo provide evidence for coadaptation of distant sites, resulting in purifying selection for intersubtype recombinants during replication.

artículo científico publicado en 2010

Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters

artículo científico publicado en 2009

Proceedings of the Frontiers of Retrovirology Conference 2016.

artículo científico publicado en 2016

Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir

artículo científico publicado en 2017

Pushing the envelope

artículo científico publicado en 2017

Quantification of HIV-1 latency reversal in resting CD4+ T cells from patients on suppressive antiretroviral therapy

artículo científico publicado en 2014

RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy

artículo científico publicado en 2009

Regimen simplification to atazanavir-ritonavir alone as maintenance antiretroviral therapy: final 48-week clinical and virologic outcomes

artículo científico publicado en 2009

Relationship between retroviral DNA-integration-site selection and host cell transcription

artículo científico publicado en 2005

Restricted replication of xenotropic murine leukemia virus-related virus in pigtailed macaques

artículo científico publicado en 2012

Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses

artículo científico publicado en 2007

Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule

artículo científico publicado en 2013

Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART.

artículo científico publicado en 2017

Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome

artículo científico publicado en 2004

Studies on the restriction of murine leukemia viruses by mouse APOBEC3

artículo científico publicado en 2012

Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy

artículo científico publicado en 2007

Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites

artículo científico publicado en 2005

The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial

artículo científico publicado en 2010

Tumors induced in mice by direct inoculation of plasmid DNA expressing both activated H-ras and c-myc

artículo científico publicado en 2010

Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase

artículo científico publicado en 2012

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

artículo científico publicado en 2016

Upregulation of CTLA-4 by HIV-specific CD4+ T cells correlates with disease progression and defines a reversible immune dysfunction

artículo científico publicado en 2007

Valproic acid without intensified antiviral therapy has limited impact on persistent HIV infection of resting CD4+ T cells

artículo científico publicado en 2008

Virions at the Gates: Receptors and the Host–Virus Arms Race ⬇️

artículo científico publicado el 28 de mayo de 2013

Virology. A new virus for old diseases?

artículo científico publicado en 2009

Virology. Weapons of mutational destruction

artículo científico publicado en 2003

Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

artículo científico publicado en 2015

Lista de obras de John Coffin

A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses

A9 A method to obtain full-length HIV proviral sequences and their sites of integration

ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia

Amplifying and quantifying HIV-1 RNA in HIV infected individuals with viral loads below the limit of detection by standard clinical assays

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Antiretroviral intensification and valproic acid lack sustained effect on residual HIV-1 viremia or resting CD4+ cell infection

Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class

Characterization of hortulanus endogenous murine leukemia virus, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup

Characterization, mapping, and distribution of the two XMRV parental proviruses

Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans

Clonal sequences recovered from plasma from patients with residual HIV-1 viremia and on intensified antiretroviral therapy are identical to replicating viral RNAs recovered from circulating resting CD4+ T cells

Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo

Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors

Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences

Correction: The Effect of Raltegravir Intensification on Low-level Residual Viremia in HIV-Infected Patients on Antiretroviral Therapy: A Randomized Controlled Trial.

Depletion of latent HIV-1 infection in vivo: a proof-of-concept study

Early Emergence and Long-Term Persistence of HIV-Infected T-Cell Clones in Children

Endogenous non-retroviral RNA virus elements in mammalian genomes

Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

Evaluation of the pathogenesis of decreasing CD4(+) T cell counts in human immunodeficiency virus type 1-infected patients receiving successfully suppressive antiretroviral therapy

Failure to confirm XMRV/MLVs in the blood of patients with chronic fatigue syndrome: a multi-laboratory study

Flexible use of nuclear import pathways by HIV-1.

Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase

Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy

HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus

HIV Pathogenesis: Dynamics and Genetics of Viral Populations and Infected Cells ⬇️

HIV-1 continues to replicate and evolve in patients with natural control of HIV infection

HIV-1 expression within resting CD4+ T cells after multiple doses of vorinostat

HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy

HIV-1 infection leads to increased transcription of human endogenous retrovirus HERV-K (HML-2) proviruses in vivo but not to increased virion production

Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection

Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy

Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance

Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients

Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy

Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults

Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control

Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule

Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision

Mouse DNA contamination in human tissue tested for XMRV

Multi-site adaptation in the presence of infrequent recombination

Multiple sources of contamination in samples from patients reported to have XMRV infection

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

Mutations in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine resistance

New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma

No evidence of HIV replication in children on antiretroviral therapy.

Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways

Ongoing HIV Replication During ART Reconsidered

Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data

Patterns of Human Immunodeficiency Virus type 1 recombination ex vivo provide evidence for coadaptation of distant sites, resulting in purifying selection for intersubtype recombinants during replication.

Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters

Proceedings of the Frontiers of Retrovirology Conference 2016.

Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir

Pushing the envelope

Quantification of HIV-1 latency reversal in resting CD4+ T cells from patients on suppressive antiretroviral therapy

RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy

Regimen simplification to atazanavir-ritonavir alone as maintenance antiretroviral therapy: final 48-week clinical and virologic outcomes

Relationship between retroviral DNA-integration-site selection and host cell transcription

Restricted replication of xenotropic murine leukemia virus-related virus in pigtailed macaques

Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses

Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule

Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART.

Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome

Studies on the restriction of murine leukemia viruses by mouse APOBEC3

Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy

Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites

The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial

Tumors induced in mice by direct inoculation of plasmid DNA expressing both activated H-ras and c-myc

Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

Upregulation of CTLA-4 by HIV-specific CD4+ T cells correlates with disease progression and defines a reversible immune dysfunction

Valproic acid without intensified antiviral therapy has limited impact on persistent HIV infection of resting CD4+ T cells

Virions at the Gates: Receptors and the Host–Virus Arms Race ⬇️

Virology. A new virus for old diseases?

Virology. Weapons of mutational destruction

Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy