John M. Coffin

Publications

• Restricted Replication of Xenotropic Murine Leukemia Virus-Related Virus in Pigtailed Macaques
  Journal of Virology. Jan, 2012  |   Pubmed ID: 22238316
• Characterization, Mapping, and Distribution of the Two XMRV Parental Proviruses
  Journal of Virology. Jan, 2012  |   Pubmed ID: 22031947
• Endogenous Murine Leukemia Viruses: Relationship to XMRV and Related Sequences Detected in Human DNA Samples
  Advances in Virology. 2011  |   Pubmed ID: 22312358
• Short-course Combivir After Single-dose Nevirapine Reduces but Does Not Eliminate the Emergence of Nevirapine Resistance in Women
  Antiviral Therapy. Nov, 2011  |   Pubmed ID: 22293443
• Binding of More Than One Tva800 Molecule is Required for ASLV-A Entry
  Retrovirology. 2011  |   Pubmed ID: 22099981
• Identification, Characterization, and Comparative Genomic Distribution of the HERV-K (HML-2) Group of Human Endogenous Retroviruses
  Retrovirology. 2011  |   Pubmed ID: 22067224
• Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: a Multi-laboratory Study
  Science (New York, N.Y.). Nov, 2011  |   Pubmed ID: 21940862
• 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. Jul, 2011  |   Pubmed ID: 21690402
• Recombinant Origin of the Retrovirus XMRV
  Science (New York, N.Y.). Jul, 2011  |   Pubmed ID: 21628392
• 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. May, 2011  |   Pubmed ID: 21576473
• 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. Apr, 2011  |   Pubmed ID: 21436045
• 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
  Journal of Virology. May, 2011  |   Pubmed ID: 21367910
• The Blood Xenotropic Murine Leukemia Virus-Related Virus Scientific Research Working Group: Mission, Progress, and Plans
  Transfusion. Mar, 2011  |   Pubmed ID: 21366602
• Genetic Diversity of Simian Immunodeficiency Virus Encoding HIV-1 Reverse Transcriptase Persists in Macaques Despite Antiretroviral Therapy
  Journal of Virology. Jan, 2011  |   Pubmed ID: 21084490
• Contamination of Human DNA Samples with Mouse DNA Can Lead to False Detection of XMRV-like Sequences
  Retrovirology. 2010  |   Pubmed ID: 21171973
• Mouse DNA Contamination in Human Tissue Tested for XMRV
  Retrovirology. 2010  |   Pubmed ID: 21171966
• HIV-1 Continues to Replicate and Evolve in Patients with Natural Control of HIV Infection
  Journal of Virology. Dec, 2010  |   Pubmed ID: 20926564
• The Effect of Raltegravir Intensification on Low-level Residual Viremia in HIV-infected Patients on Antiretroviral Therapy: a Randomized Controlled Trial
  PLoS Medicine. 2010  |   Pubmed ID: 20711481
• 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
  Journal of Virology. Aug, 2010  |   Pubmed ID: 20504919
• Comparison of Standard PCR/cloning to Single Genome Sequencing for Analysis of HIV-1 Populations
  Journal of Virological Methods. Sep, 2010  |   Pubmed ID: 20451557
• Tumors Induced in Mice by Direct Inoculation of Plasmid DNA Expressing Both Activated H-ras and C-myc
  International Journal of Biological Sciences. 2010  |   Pubmed ID: 20376206
• Flexible Use of Nuclear Import Pathways by HIV-1
  Cell Host & Microbe. Mar, 2010  |   Pubmed ID: 20227665
• Antiretroviral Intensification and Valproic Acid Lack Sustained Effect on Residual HIV-1 Viremia or Resting CD4+ Cell Infection
  PloS One. 2010  |   Pubmed ID: 20186346
• Multi-site Adaptation in the Presence of Infrequent Recombination
  Theoretical Population Biology. May, 2010  |   Pubmed ID: 20149814
• Low Frequency Nonnucleoside Reverse-transcriptase Inhibitor-resistant Variants Contribute to Failure of Efavirenz-containing Regimens in Treatment- Experienced Patients
  The Journal of Infectious Diseases. Mar, 2010  |   Pubmed ID: 20102272
• Endogenous Non-retroviral RNA Virus Elements in Mammalian Genomes
  Nature. Jan, 2010  |   Pubmed ID: 20054395
• Optimization of Allele-specific PCR Using Patient-specific HIV Consensus Sequences for Primer Design
  Journal of Virological Methods. Mar, 2010  |   Pubmed ID: 19948190
• RT-SHIV Subpopulation Dynamics in Infected Macaques During Anti-HIV Therapy
  Retrovirology. 2009  |   Pubmed ID: 19889213
• Virology. A New Virus for Old Diseases?
  Science (New York, N.Y.). Oct, 2009  |   Pubmed ID: 19815721
• Persistent Low-level Viremia in HIV-1 Elite Controllers and Relationship to Immunologic Parameters
  The Journal of Infectious Diseases. Sep, 2009  |   Pubmed ID: 19656066
• 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. Aug, 2009  |   Pubmed ID: 19628694
• Likely Role of APOBEC3G-mediated G-to-A Mutations in HIV-1 Evolution and Drug Resistance
  PLoS Pathogens. Apr, 2009  |   Pubmed ID: 19343218
• Regimen Simplification to Atazanavir-ritonavir Alone As Maintenance Antiretroviral Therapy: Final 48-week Clinical and Virologic Outcomes
  The Journal of Infectious Diseases. Mar, 2009  |   Pubmed ID: 19191590
• Lytic Granule Loading of CD8+ T Cells is Required for HIV-infected Cell Elimination Associated with Immune Control
  Immunity. Dec, 2008  |   Pubmed ID: 19062316
• Attenuation by a Thousand Cuts
  The New England Journal of Medicine. Nov, 2008  |   Pubmed ID: 19020330
• Host-retrovirus Arms Race: Trimming the Budget
  Cell Host & Microbe. Sep, 2008  |   Pubmed ID: 18779045
• Effects of Retroviruses on Host Genome Function
  Annual Review of Genetics. 2008  |   Pubmed ID: 18694346
• 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. Aug, 2008  |   Pubmed ID: 18667707
• Valproic Acid Without Intensified Antiviral Therapy Has Limited Impact on Persistent HIV Infection of Resting CD4+ T Cells
  AIDS (London, England). Jun, 2008  |   Pubmed ID: 18525258
• Interactions of Murine APOBEC3 and Human APOBEC3G with Murine Leukemia Viruses
  Journal of Virology. Jul, 2008  |   Pubmed ID: 18448535
• 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. Mar, 2008  |   Pubmed ID: 18332425
• Frequent Polymorphism at Drug Resistance Sites in HIV-1 Protease and Reverse Transcriptase
  AIDS (London, England). Feb, 2008  |   Pubmed ID: 18301062
• 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. May, 2008  |   Pubmed ID: 18218323
• Role of APOBEC3 in Genetic Diversity Among Endogenous Murine Leukemia Viruses
  PLoS Genetics. Oct, 2007  |   Pubmed ID: 17967065
• Upregulation of CTLA-4 by HIV-specific CD4+ T Cells Correlates with Disease Progression and Defines a Reversible Immune Dysfunction
  Nature Immunology. Nov, 2007  |   Pubmed ID: 17906628
• Suppression of Viremia and Evolution of Human Immunodeficiency Virus Type 1 Drug Resistance in a Macaque Model for Antiretroviral Therapy
  Journal of Virology. Nov, 2007  |   Pubmed ID: 17855539
• ART Suppresses Plasma HIV-1 RNA to a Stable Set Point Predicted by Pretherapy Viremia
  PLoS Pathogens. Apr, 2007  |   Pubmed ID: 17411338
• 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. Jan, 2007  |   Pubmed ID: 17179211
• Blinded, Multicenter Comparison of Methods to Detect a Drug-resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency
  Journal of Clinical Microbiology. Jul, 2006  |   Pubmed ID: 16825395
• Selection and Persistence of Non-nucleoside Reverse Transcriptase Inhibitor-resistant HIV-1 in Patients Starting and Stopping Non-nucleoside Therapy
  AIDS (London, England). Mar, 2006  |   Pubmed ID: 16514300
• Evolution of Broad Host Range in Retroviruses Leads to Cell Death Mediated by Highly Cytopathic Variants
  Journal of Virology. Jan, 2006  |   Pubmed ID: 16378958
• Human Endogenous Retroviral Elements As Indicators of Ectopic Recombination Events in the Primate Genome
  Genetics. Nov, 2005  |   Pubmed ID: 16157677
• Depletion of Latent HIV-1 Infection in Vivo: a Proof-of-concept Study
  Lancet. Aug 13-19, 2005  |   Pubmed ID: 16099290
• Characterization of Hortulanus Endogenous Murine Leukemia Virus, an Endogenous Provirus That Encodes an Infectious Murine Leukemia Virus of a Novel Subgroup
  Journal of Virology. Jul, 2005  |   Pubmed ID: 15956577
• 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. Apr, 2005  |   Pubmed ID: 15802467
• 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. Feb, 2005  |   Pubmed ID: 15684061
• Relationship Between Retroviral DNA-integration-site Selection and Host Cell Transcription
  Proceedings of the National Academy of Sciences of the United States of America. Feb, 2005  |   Pubmed ID: 15659548
• Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-experienced Patients Are Missed by Standard Genotype Analysis
  Journal of Clinical Microbiology. Jan, 2005  |   Pubmed ID: 15635002
• 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
  Journal of Virology. Dec, 2004  |   Pubmed ID: 15564466
• Evolution of Retroviruses: Fossils in Our DNA
  Proceedings of the American Philosophical Society. Sep, 2004  |   Pubmed ID: 15551500
• Single-strand Specificity of APOBEC3G Accounts for Minus-strand Deamination of the HIV Genome
  Nature Structural & Molecular Biology. May, 2004  |   Pubmed ID: 15098018
• 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. Feb, 2004  |   Pubmed ID: 14757818
• 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. Jan, 2004  |   Pubmed ID: 14707263
• 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. Oct, 2003  |   Pubmed ID: 14532178
• Virology. Weapons of Mutational Destruction
  Science (New York, N.Y.). Aug, 2003  |   Pubmed ID: 12920286
• Mechanisms of Avian Retroviral Host Range Extension
  Journal of Virology. Jun, 2003  |   Pubmed ID: 12767991
• The Solitary Wave of Asexual Evolution
  Proceedings of the National Academy of Sciences of the United States of America. Jan, 2003  |   Pubmed ID: 12525686
• A Novel Endogenous Retrovirus-related Element in the Human Genome Resembles a DNA Transposon: Evidence for an Evolutionary Link?
  Genomics. Nov, 2002  |   Pubmed ID: 12408960
• Proposed Alternatives for the Use of Anti-HIV Drugs: is It Appropriate?
  Drug Resistance Updates : Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy. Feb, 1999  |   Pubmed ID: 11504471