All Stories

  1. HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA

    Article • Proceedings of the National Academy of Sciences, August 2024, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  2. Widespread expression of the ancient HERV-K (HML-2) provirus group in normal human tissues

    Article • PLoS Biology, October 2022, PLOS

    Professor John M Coffin

  3. HIV proviral DNA integration can drive T cell growth ex vivo

    Article • Proceedings of the National Academy of Sciences, December 2020, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  4. Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation

    Article • Journal of Virology, October 2017, ASM Journals

    Professor John M Coffin

  5. RNA editing, epitranscriptomics, and processing in cancer progression

    Article • Cancer Biology & Therapy, December 2014, Taylor & Francis

    Professor John M Coffin

  6. A Mouse Strain Defective in Both T Cells and NK Cells Has Enhanced Sensitivity to Tumor Induction by Plasmid DNA Expressing Both Activated H-Ras and c-Myc

    Article • PLoS ONE, October 2014, PLOS

    Professor John M Coffin

  7. The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controls

    Article • Retrovirology, August 2014, Springer Science + Business Media

    Professor John M Coffin

  8. HIV-1 Infection Leads to Increased Transcription of Human Endogenous Retrovirus HERV-K (HML-2) Proviruses In Vivo but Not to Increased Virion Production

    Article • Journal of Virology, July 2014, ASM Journals

    Professor John M Coffin

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

    Article • Journal of Virological Methods, July 2014, Elsevier

    Professor John M Coffin

  10. Retrovirus Variation and Evolution

    Article • April 2014, ASM Journals

    Professor John M Coffin

  11. Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy

    Article • PLoS Pathogens, March 2014, PLOS

    Professor John M Coffin

  12. Endogenous Retroviruses and Human Cancer: Is There Anything to the Rumors?

    Article • Cell Host & Microbe, March 2014, Elsevier

    Professor John M Coffin

  13. Fifteen Years Later: Hard and Soft Selection Sweeps Confirm a Large Population Number for HIV In Vivo

    Article • PLoS Genetics, February 2014, PLOS

    Professor John M Coffin

  14. False-Positive HIV PCR Test Following Ex Vivo Lentiviral Gene Transfer Treatment of X-linked Severe Combined Immunodeficiency Vector

    Article • February 2014, Elsevier

    Professor John M Coffin

  15. The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controls

    Article • Retrovirology, January 2014, Springer Science + Business Media

    Professor John M Coffin

  16. A Novel Recombinant Retrovirus in the Genomes of Modern Birds Combines Features of Avian and Mammalian Retroviruses

    Article • Journal of Virology, December 2013, ASM Journals

    Professor John M Coffin

  17. 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

    Article • PLoS Pathogens, June 2013, PLOS

    Professor John M Coffin

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

    Article • PLoS Biology, May 2013, PLOS

    Professor John M Coffin

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

    Article • Retrovirology, February 2013, Springer Science + Business Media

    Professor John M Coffin

  20. HIV Population Dynamics

    Article • January 2013, Springer Science + Business Media

    Professor John M Coffin

  21. Betaretroviral Envelope Subunits Are Noncovalently Associated and Restricted to the Mammalian Class

    Article • Journal of Virology, December 2012, ASM Journals

    Professor John M Coffin

  22. HIV-1 Pathogenesis: The Virus

    Article • Cold Spring Harbor Perspectives in Medicine, November 2012, Cold Spring Harbor Laboratory Press

    Professor John M Coffin

  23. A Multicenter Blinded Analysis Indicates No Association between Chronic Fatigue Syndrome/Myalgic Encephalomyelitis and either Xenotropic Murine Leukemia Virus-Related Virus or Polytropic Murine Leukemia Virus

    Article • mBio, September 2012, ASM Journals

    Professor John M Coffin, Professor Walter Ian Lipkin

  24. Ultrasensitive Allele-Specific PCR Reveals Rare Preexisting Drug-Resistant Variants

    Article • Journal of Virology, August 2012, ASM Journals

    Professor John M Coffin, Dr Zandrea Ambrose

  25. Recombinant origin, contamination, and de-discovery of XMRV

    Article • Current Opinion in Virology, August 2012, Elsevier

    Professor John M Coffin

  26. Studies on the Restriction of Murine Leukemia Viruses by Mouse APOBEC3

    Article • PLoS ONE, May 2012, PLOS

    Professor John M Coffin

  27. Multiple Sources of Contamination in Samples from Patients Reported to Have XMRV Infection

    Article • PLoS ONE, February 2012, PLOS

    Professor John M Coffin

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

    Article • Journal of Virology, January 2012, ASM Journals

    Professor John M Coffin

  29. From XMRV to HIV-1 and back

    Article • Retrovirology, October 2011, Springer Science + Business Media

    Professor John M Coffin

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

    Article • Retrovirology, October 2011, Springer Science + Business Media

    Professor John M Coffin

  31. Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays

    Article • Journal of Visualized Experiments, September 2011, MyJove Corporation

    Professor John M Coffin

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

    Article • PLoS Medicine, August 2011, PLOS

    Professor John M Coffin

  33. Multi-laboratory evaluations of XMRV nucleic acid detection assays

    Article • Retrovirology, June 2011, Springer Science + Business Media

    Professor John M Coffin

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

    Article • Transfusion, March 2011, Wiley

    Professor John M Coffin

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

    Article • Retrovirology, January 2011, Springer Science + Business Media

    Professor John M Coffin

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

    Article • Retrovirology, January 2011, Springer Science + Business Media

    Professor John M Coffin

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

    Article • Advances in Virology, January 2011, Hindawi Publishing Corporation

    Professor John M Coffin

  38. ART did not decrease genetic diversity of RT-SHIV

    Article • Journal of Virology, November 2010, ASM Journals

    Professor John M Coffin, Dr Zandrea Ambrose

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

    Article • PLoS Medicine, August 2010, PLOS

    Professor John M Coffin

  40. 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

    Article • Journal of Virology, May 2010, ASM Journals

    Professor John M Coffin

  41. Multi-site adaptation in the presence of infrequent recombination

    Article • Theoretical Population Biology, May 2010, Elsevier

    Professor John M Coffin

  42. Interpreting the effect of vaccination on steady state infection in animals challenged with Simian immunodeficiency virus

    Article • Journal of Theoretical Biology, April 2010, Elsevier

    Professor John M Coffin

  43. CPSF6 binds HIV-1 capsid and cytoplasmic expression restricts infection

    Article • Cell Host & Microbe, March 2010, Elsevier

    Dr Yuan Li, Professor John M Coffin, Dr Zandrea Ambrose

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

    Article • Journal of Virological Methods, March 2010, Elsevier

    Professor John M Coffin

  45. Antiretroviral Intensification and Valproic Acid Lack Sustained Effect on Residual HIV-1 Viremia or Resting CD4+ Cell Infection

    Article • PLoS ONE, February 2010, PLOS

    Professor John M Coffin, Dr Nancie M Archin

  46. Low Frequency Nonnucleoside Reverse‐Transcriptase Inhibitor–Resistant Variants Contribute to Failure of Efavirenz‐Containing Regimens in Treatment‐Experienced Patients

    Article • The Journal of Infectious Diseases, January 2010, Oxford University Press (OUP)

    Professor John M Coffin

  47. Endogenous non-retroviral RNA virus elements in mammalian genomes

    Article • Nature, January 2010, Springer Science + Business Media

    Professor John M Coffin

  48. Mouse DNA contamination in human tissue tested for XMRV

    Article • Retrovirology, January 2010, Springer Science + Business Media

    Professor John M Coffin

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

    Article • Retrovirology, January 2010, Springer Science + Business Media

    Professor John M Coffin

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

    Article • Retrovirology, November 2009, Springer Science + Business Media

    Professor John M Coffin, Dr Zandrea Ambrose

  51. A New Virus for Old Diseases?

    Article • Science, October 2009, American Association for the Advancement of Science

    Professor John M Coffin

  52. Persistent Low‐Level Viremia in HIV‐1 Elite Controllers and Relationship to Immunologic Parameters

    Article • The Journal of Infectious Diseases, September 2009, Oxford University Press (OUP)

    Professor John M Coffin

  53. Evaluation of the Pathogenesis of Decreasing CD4 + T Cell Counts in Human Immunodeficiency Virus Type 1–Infected Patients Receiving Successfully Suppressive Antiretroviral Therapy

    Article • The Journal of Infectious Diseases, June 2009, Oxford University Press (OUP)

    Professor John M Coffin

  54. Likely Role of APOBEC3G-Mediated G-to-A Mutations in HIV-1 Evolution and Drug Resistance

    Article • PLoS Pathogens, April 2009, PLOS

    Professor John M Coffin

  55. Regimen Simplification to Atazanavir‐Ritonavir Alone as Maintenance Antiretroviral Therapy: Final 48‐Week Clinical and Virologic Outcomes

    Article • The Journal of Infectious Diseases, March 2009, Oxford University Press (OUP)

    Professor John M Coffin

  56. Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected Individuals

    Article • Journal of Virology, December 2008, ASM Journals

    Professor John M Coffin

  57. Effects of Retroviruses on Host Genome Function

    Article • Annual Review of Genetics, December 2008, Annual Reviews

    Professor John M Coffin

  58. Attenuation by a Thousand Cuts

    Article • New England Journal of Medicine, November 2008, New England Journal of Medicine (NEJM/MMS)

    Professor John M Coffin

  59. Host-Retrovirus Arms Race: Trimming the Budget

    Article • Cell Host & Microbe, September 2008, Elsevier

    Professor John M Coffin

  60. Detection of Nonnucleoside Reverse‐Transcriptase Inhibitor–Resistant HIV‐1 after Discontinuation of Virologically Suppressive Antiretroviral Therapy

    Article • Clinical Infectious Diseases, August 2008, Oxford University Press (OUP)

    Professor John M Coffin

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

    Article • AIDS, June 2008, Wolters Kluwer Health

    Professor John M Coffin, Dr Nancie M Archin

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

    Article • AIDS, February 2008, Wolters Kluwer Health

    Professor John M Coffin

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

    Article • Nature Immunology, September 2007, Springer Science + Business Media

    Dr Mark A Brockman, Professor John M Coffin

  64. Study of RT inhibitor resistance in a macaque model of HIV/AIDS

    Article • Journal of Virology, September 2007, ASM Journals

    Professor John M Coffin, Dr Zandrea Ambrose

  65. Retroviruses and AIDS: evolution and drug resistance

    Article • Future HIV Therapy, September 2007, Future Medicine

    Professor John M Coffin

  66. Role of APOBEC3 in Genetic Diversity among Endogenous Murine Leukemia Viruses

    Article • PLoS Genetics, January 2007, PLOS

    Professor John M Coffin

  67. ART Suppresses Plasma HIV-1 RNA to a Stable Set Point Predicted by Pretherapy Viremia

    Article • PLoS Pathogens, January 2007, PLOS

    Professor John M Coffin

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

    Article • AIDS, March 2006, Wolters Kluwer Health

    Professor John M Coffin

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

    Article • The Lancet, August 2005, Elsevier

    Professor John M Coffin

  70. Characterization of Hortulanus Endogenous Murine Leukemia Virus, an Endogenous Provirus That Encodes an Infectious Murine Leukemia Virus of a Novel Subgroup

    Article • Journal of Virology, July 2005, ASM Journals

    Professor John M Coffin

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

    Article • Proceedings of the National Academy of Sciences, March 2005, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  72. Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis

    Article • Journal of Clinical Microbiology, January 2005, ASM Journals

    Professor John M Coffin

  73. Role of APOBEC3 in Genetic Diversity among Endogenous Murine Leukemia Viruses

    Article • PLoS Genetics, January 2005, PLOS

    Professor John M Coffin, jonathan stoye

  74. SIV containing HIV-1 RT can be inhibited by anti-HIV-1 RT inhibitors

    Article • Journal of Virology, December 2004, ASM Journals

    Professor John M Coffin, Dr Zandrea Ambrose

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

    Article • Nature Structural & Molecular Biology, April 2004, Springer Science + Business Media

    Professor John M Coffin

  76. New Real-Time Reverse Transcriptase-Initiated PCR Assay with Single-Copy Sensitivity for Human Immunodeficiency Virus Type 1 RNA in Plasma

    Article • Journal of Clinical Microbiology, October 2003, ASM Journals

    Professor John M Coffin

  77. A Novel Endogenous Retrovirus-Related Element in the Human Genome Resembles a DNA Transposon: Evidence for an Evolutionary Link?

    Article • Genomics, November 2002, Elsevier

    Professor John M Coffin

  78. Mouse Mammary Tumor Virus Superantigen Expression Is Reduced by Glucocorticoid Treatment

    Article • Virology, September 2000, Elsevier

    Professor John M Coffin

  79. The Mouse Mammary Tumor Virus Transcription Enhancers for Hematopoietic Progenitor and Mammary Gland Cells Share Functional Elements

    Article • Journal of Virology, September 2000, ASM Journals

    Professor John M Coffin

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

    Article • Drug Resistance Updates, February 1999, Elsevier

    Professor John M Coffin

  81. Book Review Microbe Hunters — Then and now Edited by Hilary Koprowski and Michael B.A. Oldstone. 456 pp., illustrated. Bloomington, Ill., Medi-Ed Press, 1996. $45. 0-936741-11-2

    Article • New England Journal of Medicine, April 1997, New England Journal of Medicine (NEJM/MMS)

    Professor John M Coffin

  82. Workshop Summary : Workshop on Perinatally Acquired Human Immunodeficiency Virus Infection in Long-Term Surviving Children: A Collaborative Study of Factors Contributing to Slow Disease Progression

    Article • AIDS Research and Human Retroviruses, November 1996, Mary Ann Liebert Inc

    Professor John M Coffin

  83. Retrovirus restriction revealed

    Article • Nature, August 1996, Springer Science + Business Media

    Professor John M Coffin

  84. The dangers of xenotransplantation

    Article • Nature Medicine, November 1995, Springer Science + Business Media

    Professor John M Coffin, jonathan stoye

  85. Stimulation of mouse mammary tumor virus superantigen expression by an intragenic enhancer.

    Article • Proceedings of the National Academy of Sciences, September 1995, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  86. Lines drawn in epitope wars

    Article • Nature, June 1995, Springer Science + Business Media

    Professor John M Coffin

  87. Multifactorial inheritance of neural tube defects: localization of the major gene and recognition of modifiers in ct mutant mice

    Article • Nature Genetics, April 1994, Springer Science + Business Media

    Professor John M Coffin

  88. How does variation count?

    Article • Nature, September 1992, Springer Science + Business Media

    Professor John M Coffin

  89. Mapping of the motor neuron degeneration (Mnd) gene, a mouse model of amyotrophic lateral sclerosis (ALS)

    Article • Genomics, July 1992, Elsevier

    Professor John M Coffin

  90. Mechanism of transduction by retroviruses

    Article • Science, February 1992, American Association for the Advancement of Science

    Professor John M Coffin

  91. Superantigens and endogenous retroviruses: a confluence of puzzles

    Article • Science, January 1992, American Association for the Advancement of Science

    Professor John M Coffin

  92. Structure and Classification of Retroviruses

    Article • January 1992, Springer Science + Business Media

    Professor John M Coffin

  93. Characterization of the endogenous nonecotropic murine leukemia viruses of NZB/BINJ and SM/J inbred strains

    Article • Mammalian Genome, January 1992, Springer Science + Business Media

    Professor John M Coffin

  94. Book Review Virus Hunting: AIDS, cancer, and the human retrovirus By Robert Gallo. 352 pp., illustrated. New York, Basic Books, 1991. $22.95.

    Article • New England Journal of Medicine, August 1991, New England Journal of Medicine (NEJM/MMS)

    Professor John M Coffin

  95. Linkage of Mls genes to endogenous mammary tumour viruses of inbred mice

    Article • Nature, February 1991, Springer Science + Business Media

    Professor John M Coffin

  96. Isotype switching of an immunoglobulin heavy chain transgene occurs by DNA recombination between different chromosomes

    Article • Cell, November 1990, Elsevier

    Professor John M Coffin

  97. Molecular mechanisms of nucleic acid integration

    Article • Journal of Medical Virology, May 1990, Wiley

    Professor John M Coffin

  98. The virology of AIDS

    Article • AIDS, January 1990, Wolters Kluwer Health

    Professor John M Coffin

  99. Genetic Variation in Retroviruses

    Article • January 1990, Springer Science + Business Media

    Professor John M Coffin

  100. Determination of 3′ end processing in retroelements

    Article • Trends in Genetics, January 1990, Elsevier

    Professor John M Coffin

  101. Genetics of Endogenous Murine Leukemia Viruses

    Article • Annals of the New York Academy of Sciences, August 1989, Wiley

    Professor John M Coffin

  102. Too high a price

    Article • Nature, July 1989, Springer Science + Business Media

    Professor John M Coffin

  103. Role of endogenous retroviruses as mutagens: The hairless mutation of mice

    Article • Cell, July 1988, Elsevier

    Professor John M Coffin, jonathan stoye

  104. Highly preferred targets for retrovirus integration

    Article • Cell, May 1988, Elsevier

    Professor John M Coffin

  105. Rous sarcoma virus is integrated but not expressed in chicken early embryonic cells.

    Article • Proceedings of the National Academy of Sciences, May 1987, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  106. Genetic variation in AIDS viruses

    Article • Cell, July 1986, Elsevier

    Professor John M Coffin

  107. Microbiology: The Microbe 1984.

    Article • Science, January 1985, American Association for the Advancement of Science

    Professor John M Coffin

  108. Genomes of endogenous and exogenous avian retroviruses

    Article • Virology, April 1983, Elsevier

    Professor John M Coffin

  109. VARIATION IN AVIAN RETROVIRUS GENOMES

    Article • Annals of the New York Academy of Sciences, November 1980, Wiley

    Professor John M Coffin

  110. Structural Analysis of Retrovirus Genomes

    Article • January 1980, Elsevier

    Professor John M Coffin

  111. VIRAL ENVELOPE GENES AND c REGIONS IN NON-ACUTE AVIAN LEUKOSIS VIRUS ASSOCIATED DISEASE

    Article • January 1980, Elsevier

    Professor John M Coffin

  112. SYNTHESIS AND PROCESSING OF THE INTERNAL STRUCTURAL PROTEINS OF RETROVIRUSES: SITE OF SYNTHESIS, EVIDENCE FOR MULTIPLY-CHARGED SPECIES, AND ANALYSIS OF A MUTANT DEFECTIVE IN PROCESSING11This research supported by grants from the National Cancer Institu...

    Article • January 1980, Elsevier

    Professor John M Coffin

  113. Subgroup-E Avian-leukosis-virus-associated Disease in Chickens

    Article • Cold Spring Harbor Symposia on Quantitative Biology, January 1980, Cold Spring Harbor Laboratory Press

    Professor John M Coffin

  114. Recombination between the defective component of an acute leukemia virus and Rous associated virus O, an endogenous virus of chickens.

    Article • Proceedings of the National Academy of Sciences, June 1979, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  115. In Vitro Studies of the Replication of Moloney Murine Leukemia Virus

    Article • Cold Spring Harbor Symposia on Quantitative Biology, January 1979, Cold Spring Harbor Laboratory Press

    Professor John M Coffin

  116. Recombinant avian oncoviruses I. Alterations in the precursor to the internal structural proteins

    Article • Virology, June 1978, Elsevier

    Professor John M Coffin

  117. Structure of the genome of moloney murine leukemia virus: a terminally redundant sequence

    Article • Cell, April 1978, Elsevier

    Professor John M Coffin

  118. Nucleotide sequence of Rous sarcoma virus RNA at the initiation site of DNA synthesis

    Article • Journal of Molecular Biology, December 1977, Elsevier

    Professor John M Coffin

  119. The genome of Uukuniemi virus consists of three unique RNA segments

    Article • Cell, May 1977, Elsevier

    Professor John M Coffin

  120. Terminal redundancy and the origin of replication of Rous sarcoma virus RNA.

    Article • Proceedings of the National Academy of Sciences, May 1977, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  121. A physical map of the Rous sarcoma virus genome

    Article • Journal of Molecular Biology, January 1976, Elsevier

    Professor John M Coffin

  122. The Nucleotide Sequence Complexity of Avian Tumor Virus RNA

    Article • Proceedings of the National Academy of Sciences, September 1974, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  123. In Vitro Synthesis of Rous Sarcoma Virus-Specific RNA is Catalyzed by a DNA-Dependent RNA Polymerase

    Article • Proceedings of the National Academy of Sciences, July 1974, Proceedings of the National Academy of Sciences

    Professor John M Coffin

  124. A new approach to the isolation of RNA-DNA hybrids and its application to the quantitative determination of labeled tumor virus RNA

    Article • Journal of Molecular Biology, June 1974, Elsevier

    Professor John M Coffin

  125. Retroviruses

    Article • Springer Science + Business Media

    Professor John M Coffin