John M. Coffin

Evolution of retroviruses: fossils in our DNA.

Proposed alternatives for the use of anti-HIV drugs: is it appropriate?

A novel endogenous retrovirus-related element in the human genome resembles a DNA transposon: evidence for an evolutionary link?

The solitary wave of asexual evolution.

Mechanisms of avian retroviral host range extension.

Virology. Weapons of mutational destruction.

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

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

Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution.

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

In vitro characterization of a simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques.

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

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

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

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

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

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

Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome.

Evolution of broad host range in retroviruses leads to cell death mediated by highly cytopathic variants.

Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.

Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency.

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

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

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

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

Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses.

Oncogenicity of DNA in vivo: tumor induction with expression plasmids for activated H-ras and c-myc.

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

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

Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses.

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

HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.

Effects of retroviruses on host genome function.

Host-retrovirus arms race: trimming the budget.

Attenuation by a thousand cuts.

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

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

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

High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis.

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

Virology. A new virus for old diseases?

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

Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design.

Endogenous non-retroviral RNA virus elements in mammalian genomes.

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

Multi-site adaptation in the presence of infrequent recombination.

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

Flexible use of nuclear import pathways by HIV-1.

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

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

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.

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

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

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

Mouse DNA contamination in human tissue tested for XMRV.

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

The Blood Xenotropic Murine Leukemia Virus-Related Virus Scientific Research Working Group: mission, progress, and plans.

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.

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

Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine.

Recombinant origin of the retrovirus XMRV.

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

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

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

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses.

Binding of more than one Tva800 molecule is required for ASLV-A entry.

Restricted Replication of Xenotropic Murine Leukemia Virus-Related Virus in Pigtailed Macaques.

Short-course Combivir after single-dose nevirapine reduces but does not eliminate the emergence of nevirapine resistance in women.

Endogenous Murine Leukemia Viruses: Relationship to XMRV and Related Sequences Detected in Human DNA Samples.