John M. Coffin

Department of Molecular Biology and Microbiology, Tuffts University

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 10	2011

Other Publications

Article	Year
Evolution of retroviruses: fossils in our DNA. Proceedings of the American Philosophical Society\| PubMed ID: 15551500	2004
Proposed alternatives for the use of anti-HIV drugs: is it appropriate? Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy\| PubMed ID: 11504471	1999
A novel endogenous retrovirus-related element in the human genome resembles a DNA transposon: evidence for an evolutionary link? Genomics\| PubMed ID: 12408960	2002
The solitary wave of asexual evolution. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12525686	2003
Mechanisms of avian retroviral host range extension. Journal of virology\| PubMed ID: 12767991	2003
Virology. Weapons of mutational destruction. Science (New York, N.Y.)\| PubMed ID: 12920286	2003
New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma. Journal of clinical microbiology\| PubMed ID: 14532178	2003
Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 14707263	2004
Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 14757818	2004
Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nature structural & molecular biology\| PubMed ID: 15098018	2004
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 m... Journal of virology\| PubMed ID: 15564466	2004
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. Journal of clinical microbiology\| PubMed ID: 15635002	2005
Relationship between retroviral DNA-integration-site selection and host cell transcription. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15659548	2005
Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15684061	2005
Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15802467	2005
Characterization of hortulanus endogenous murine leukemia virus, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup. Journal of virology\| PubMed ID: 15956577	2005
Depletion of latent HIV-1 infection in vivo: a proof-of-concept study. Lancet\| PubMed ID: 16099290	2005
Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome. Genetics\| PubMed ID: 16157677	2005
Evolution of broad host range in retroviruses leads to cell death mediated by highly cytopathic variants. Journal of virology\| PubMed ID: 16378958	2006
Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy. AIDS (London, England)\| PubMed ID: 16514300	2006
Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. Journal of clinical microbiology\| PubMed ID: 16825395	2006
Mutations in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine resistance. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17179211	2007
ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS pathogens\| PubMed ID: 17411338	2007
Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy. Journal of virology\| PubMed ID: 17855539	2007
Upregulation of CTLA-4 by HIV-specific CD4+ T cells correlates with disease progression and defines a reversible immune dysfunction. Nature immunology\| PubMed ID: 17906628	2007
Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses. PLoS genetics\| PubMed ID: 17967065	2007
Oncogenicity of DNA in vivo: tumor induction with expression plasmids for activated H-ras and c-myc. Biologicals : journal of the International Association of Biological Standardization\| PubMed ID: 18218323	2008
Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase. AIDS (London, England)\| PubMed ID: 18301062	2008
Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18332425	2008
Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses. Journal of virology\| PubMed ID: 18448535	2008
Valproic acid without intensified antiviral therapy has limited impact on persistent HIV infection of resting CD4+ T cells. AIDS (London, England)\| PubMed ID: 18525258	2008
HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18667707	2008
Effects of retroviruses on host genome function. Annual review of genetics\| PubMed ID: 18694346	2008
Host-retrovirus arms race: trimming the budget. Cell host & microbe\| PubMed ID: 18779045	2008
Attenuation by a thousand cuts. The New England journal of medicine\| PubMed ID: 19020330	2008
Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control. Immunity\| PubMed ID: 19062316	2008
Regimen simplification to atazanavir-ritonavir alone as maintenance antiretroviral therapy: final 48-week clinical and virologic outcomes. The Journal of infectious diseases\| PubMed ID: 19191590	2009
Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance. PLoS pathogens\| PubMed ID: 19343218	2009
High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19628694	2009
Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters. The Journal of infectious diseases\| PubMed ID: 19656066	2009
Virology. A new virus for old diseases? Science (New York, N.Y.)\| PubMed ID: 19815721	2009
RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy. Retrovirology\| PubMed ID: 19889213	2009
Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design. Journal of virological methods\| PubMed ID: 19948190	2010
Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature\| PubMed ID: 20054395	2010
Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients. The Journal of infectious diseases\| PubMed ID: 20102272	2010
Multi-site adaptation in the presence of infrequent recombination. Theoretical population biology\| PubMed ID: 20149814	2010
Antiretroviral intensification and valproic acid lack sustained effect on residual HIV-1 viremia or resting CD4+ cell infection. PloS one\| PubMed ID: 20186346	2010
Flexible use of nuclear import pathways by HIV-1. Cell host & microbe\| PubMed ID: 20227665	2010
Tumors induced in mice by direct inoculation of plasmid DNA expressing both activated H-ras and c-myc. International journal of biological sciences\| PubMed ID: 20376206	2010
Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations. Journal of virological methods\| PubMed ID: 20451557	2010
Patterns of Human Immunodeficiency Virus type 1 recombination ex vivo provide evidence for coadaptation of distant sites, resulting in purifying selection for intersubtype recombinants durin... Journal of virology\| PubMed ID: 20504919	2010
The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial. PLoS medicine\| PubMed ID: 20711481	2010
HIV-1 continues to replicate and evolve in patients with natural control of HIV infection. Journal of virology\| PubMed ID: 20926564	2010
Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy. Journal of virology\| PubMed ID: 21084490	2011
Mouse DNA contamination in human tissue tested for XMRV. Retrovirology\| PubMed ID: 21171966	2010
Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences. Retrovirology\| PubMed ID: 21171973	2010
The Blood Xenotropic Murine Leukemia Virus-Related Virus Scientific Research Working Group: mission, progress, and plans. Transfusion\| PubMed ID: 21366602	2011
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 ... Journal of virology\| PubMed ID: 21367910	2011
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21436045	2011
Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21576473	2011
Recombinant origin of the retrovirus XMRV. Science (New York, N.Y.)\| PubMed ID: 21628392	2011
Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21690402	2011
Failure to confirm XMRV/MLVs in the blood of patients with chronic fatigue syndrome: a multi-laboratory study. Science (New York, N.Y.)\| PubMed ID: 21940862	2011
Characterization, mapping, and distribution of the two XMRV parental proviruses. Journal of virology\| PubMed ID: 22031947	2012
Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology\| PubMed ID: 22067224	2011
Binding of more than one Tva800 molecule is required for ASLV-A entry. Retrovirology\| PubMed ID: 22099981	2011
Restricted Replication of Xenotropic Murine Leukemia Virus-Related Virus in Pigtailed Macaques. Journal of virology\| PubMed ID: 22238316	2012
Short-course Combivir after single-dose nevirapine reduces but does not eliminate the emergence of nevirapine resistance in women. Antiviral therapy\| PubMed ID: 22293443	2011
Endogenous Murine Leukemia Viruses: Relationship to XMRV and Related Sequences Detected in Human DNA Samples. Advances in virology\| PubMed ID: 22312358	2011