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Last Name
Institution

John M. Coffin

TitleProfessor
InstitutionTufts University School of Medicine
DepartmentMolecular Biology and Microbiology
AddressMolecular Biology and Microbiology
Tufts University Schhol of Medicine
136 Harrison Avenue
Boston MA 02111-1800
Phone(617) 636-6528
Fax(617) 636-8086
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Montesion M, Bhardwaj N, Williams ZH, Kuperwasser C, Coffin JM. Mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation. J Virol. 2017 Oct 18. PMID: 29046454.
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    2. Van Zyl GU, Katusiime MG, Wiegand A, McManus WR, Bale MJ, Halvas EK, Luke B, Boltz VF, Spindler J, Laughton B, Engelbrecht S, Coffin JM, Cotton MF, Shao W, Mellors JW, Kearney MF. No evidence of HIV replication in children on antiretroviral therapy. J Clin Invest. 2017 Sep 11. PMID: 28891813.
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    3. Gay CL, DeBenedette MA, Tcherepanova IY, Gamble A, Lewis WE, Cope AB, Kuruc JD, McGee KS, Kearney MF, Coffin JM, Archin NM, Hicks CB, Eron JJ, Nicolette CA, Margolis DM. Immunogenicity of AGS-004 Dendritic Cell Therapy in Patients Treated During Acute HIV Infection. AIDS Res Hum Retroviruses. 2017 Jun 21. PMID: 28636433.
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    4. Gay CL, Bosch RJ, Ritz J, Hataye JM, Aga E, Tressler RL, Mason SW, Hwang CK, Grasela DM, Ray N, Cyktor JC, Coffin JM, Acosta EP, Koup RA, Mellors JW, Eron JJ. Clinical Trial of the Anti-PD-L1 Antibody BMS-936559 in HIV-1 Infected Participants on Suppressive Antiretroviral Therapy. J Infect Dis. 2017 Apr 18. PMID: 28431010.
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    5. Wiegand A, Spindler J, Hong FF, Shao W, Cyktor JC, Cillo AR, Halvas EK, Coffin JM, Mellors JW, Kearney MF. Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART. Proc Natl Acad Sci U S A. 2017 Apr 17. PMID: 28416661.
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    6. Bui JK, Sobolewski MD, Keele BF, Spindler J, Musick A, Wiegand A, Luke BT, Shao W, Hughes SH, Coffin JM, Kearney MF, Mellors JW. Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir. PLoS Pathog. 2017 Mar; 13(3):e1006283. PMID: 28328934.
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    7. Boltz VF, Rausch J, Shao W, Hattori J, Luke B, Maldarelli F, Mellors JW, Kearney MF, Coffin JM. Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA. Retrovirology. 2016 Dec 20; 13(1):87. PMID: 27998286.
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    8. Coffin JM, Fan H. The Discovery of Reverse Transcriptase. Annu Rev Virol. 2016 Sep 29; 3(1):29-51. PMID: 27482900.
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    9. Shao W, Shan J, Kearney MF, Wu X, Maldarelli F, Mellors JW, Luke B, Coffin JM, Hughes SH. Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes. Retrovirology. 2016; 13(1):47. PMID: 27377064.
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    10. Hughes SH, Coffin JM. What Integration Sites Tell Us about HIV Persistence. Cell Host Microbe. 2016 May 11; 19(5):588-98. PMID: 27173927.
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    11. Wildschutte JH, Williams ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A. 2016 Apr 19; 113(16):E2326-34. PMID: 27001843.
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    12. Simonetti FR, Sobolewski MD, Fyne E, Shao W, Spindler J, Hattori J, Anderson EM, Watters SA, Hill S, Wu X, Wells D, Su L, Luke BT, Halvas EK, Besson G, Penrose KJ, Yang Z, Kwan RW, Van Waes C, Uldrick T, Citrin DE, Kovacs J, Polis MA, Rehm CA, Gorelick R, Piatak M, Keele BF, Kearney MF, Coffin JM, Hughes SH, Mellors JW, Maldarelli F. Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo. Proc Natl Acad Sci U S A. 2016 Feb 16; 113(7):1883-8. PMID: 26858442.
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    13. Coffin JM. The discovery of HTLV-1, the first pathogenic human retrovirus. Proc Natl Acad Sci U S A. 2015 Dec 22; 112(51):15525-9. PMID: 26696625.
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    14. Kearney MF, Wiegand A, Shao W, Coffin JM, Mellors JW, Lederman M, Gandhi RT, Keele BF, Li JZ. Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy. J Virol. 2015; 90(3):1369-76. PMID: 26581989.
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    15. Kearney MF, Anderson EM, Coomer C, Smith L, Shao W, Johnson N, Kline C, Spindler J, Mellors JW, Coffin JM, Ambrose Z. Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy. Retrovirology. 2015; 12:93. PMID: 26559632.
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    16. Bhardwaj N, Montesion M, Roy F, Coffin JM. Differential Expression of HERV-K (HML-2) Proviruses in Cells and Virions of the Teratocarcinoma Cell Line Tera-1. Viruses. 2015; 7(3):939-68. PMID: 25746218.
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    17. Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Howcroft TK, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E. RNA editing, epitranscriptomics, and processing in cancer progression. Cancer Biol Ther. 2015 Jan 2; 16(1):21-7. PMID: 25455629.
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    18. Sheng-Fowler L, Tu W, Fu H, Murata H, Lanning L, Foseh G, Macauley J, Blair D, Hughes SH, Coffin JM, Lewis AM, Peden K. 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. PLoS One. 2014; 9(10):e108926. PMID: 25302710; PMCID: PMC4193875.
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    19. Cillo AR, Vagratian D, Bedison MA, Anderson EM, Kearney MF, Fyne E, Koontz D, Coffin JM, Piatak M, Mellors JW. Improved single-copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy. J Clin Microbiol. 2014 Nov; 52(11):3944-51. PMID: 25187636.
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    20. Wildschutte JH, Ram D, Subramanian R, Stevens VL, Coffin JM. The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controls. Retrovirology. 2014; 11:62. PMID: 25112280; PMCID: PMC4149278.
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    21. Bhardwaj N, Maldarelli F, Mellors J, Coffin JM. HIV-1 infection leads to increased transcription of human endogenous retrovirus HERV-K (HML-2) proviruses in vivo but not to increased virion production. J Virol. 2014 Oct; 88(19):11108-20. PMID: 25056891; PMCID: PMC4178833 [Available on 04/01/15].
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    22. Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH. HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science. 2014 Jul 11; 345(6193):179-83. PMID: 24968937.
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    23. Cillo AR, Sobolewski MD, Bosch RJ, Fyne E, Piatak M, Coffin JM, Mellors JW. Quantification of HIV-1 latency reversal in resting CD4+ T cells from patients on suppressive antiretroviral therapy. Proc Natl Acad Sci U S A. 2014 May 13; 111(19):7078-83. PMID: 24706775; PMCID: PMC4024870.
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    24. Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM. PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data. J Virol Methods. 2014 Jul; 203:73-80. PMID: 24681054; NIHMSID: NIHMS580920 [Available on 07/01/15].
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    25. Kearney MF, Spindler J, Shao W, Yu S, Anderson EM, O'Shea A, Rehm C, Poethke C, Kovacs N, Mellors JW, Coffin JM, Maldarelli F. Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy. PLoS Pathog. 2014 Mar; 10(3):e1004010. PMID: 24651464; PMCID: PMC3961343.
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    26. Bhardwaj N, Coffin JM. Endogenous retroviruses and human cancer: is there anything to the rumors? Cell Host Microbe. 2014 Mar 12; 15(3):255-9. PMID: 24629332.
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    27. Archin NM, Bateson R, Tripathy MK, Crooks AM, Yang KH, Dahl NP, Kearney MF, Anderson EM, Coffin JM, Strain MC, Richman DD, Robertson KR, Kashuba AD, Bosch RJ, Hazuda DJ, Kuruc JD, Eron JJ, Margolis DM. HIV-1 expression within resting CD4+ T cells after multiple doses of vorinostat. J Infect Dis. 2014 Sep 1; 210(5):728-35. PMID: 24620025; PMCID: PMC4148603 [Available on 09/01/15].
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    28. Rouzine IM, Coffin JM, Weinberger LS. Fifteen years later: hard and soft selection sweeps confirm a large population number for HIV in vivo. PLoS Genet. 2014 Feb; 10(2):e1004179. PMID: 24586204; PMCID: PMC3930503.
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    29. De Ravin SS, Gray JT, Throm RE, Spindler J, Kearney M, Wu X, Coffin JM, Hughes SH, Malderelli F, Sorrentino BP, Malech HL. False-positive HIV PCR test following ex vivo lentiviral gene transfer treatment of X-linked severe combined immunodeficiency vector. Mol Ther. 2014 Feb; 22(2):244-5. PMID: 24487563; PMCID: PMC3918917 [Available on 02/01/15].
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    30. Boltz VF, Bao Y, Lockman S, Halvas EK, Kearney MF, McIntyre JA, Schooley RT, Hughes MD, Coffin JM, Mellors JW. Low-frequency nevirapine (NVP)-resistant HIV-1 variants are not associated with failure of antiretroviral therapy in women without prior exposure to single-dose NVP. J Infect Dis. 2014 Mar 1; 209(5):703-10. PMID: 24443547; PMCID: PMC3923545 [Available on 03/01/15].
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    31. Henzy JE, Gifford RJ, Johnson WE, Coffin JM. A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J Virol. 2014 Mar; 88(5):2398-405. PMID: 24352464; PMCID: PMC3958055.
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    32. Delviks-Frankenberry K, Paprotka T, Cingöz O, Wildt S, Hu WS, Coffin JM, Pathak VK. Generation of multiple replication-competent retroviruses through recombination between PreXMRV-1 and PreXMRV-2. J Virol. 2013 Nov; 87(21):11525-37. PMID: 23966380; PMCID: PMC3807343.
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    33. Josefsson L, Palmer S, Faria NR, Lemey P, Casazza J, Ambrozak D, Kearney M, Shao W, Kottilil S, Sneller M, Mellors J, Coffin JM, Maldarelli F. 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. PLoS Pathog. 2013; 9(6):e1003432. PMID: 23818847; PMCID: PMC3688524.
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    34. Coffin JM. Virions at the gates: receptors and the host-virus arms race. PLoS Biol. 2013; 11(5):e1001574. PMID: 23723739; PMCID: PMC3665852.
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    35. Maldarelli F, Kearney M, Palmer S, Stephens R, Mican J, Polis MA, Davey RT, Kovacs J, Shao W, Rock-Kress D, Metcalf JA, Rehm C, Greer SE, Lucey DL, Danley K, Alter H, Mellors JW, Coffin JM. HIV populations are large and accumulate high genetic diversity in a nonlinear fashion. J Virol. 2013 Sep; 87(18):10313-23. PMID: 23678164; PMCID: PMC3754011.
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    36. Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology. 2013; 10:18. PMID: 23402264; PMCID: PMC3599717.
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    37. Coffin J, Swanstrom R. HIV pathogenesis: dynamics and genetics of viral populations and infected cells. Cold Spring Harb Perspect Med. 2013 Jan; 3(1):a012526. PMID: 23284080.
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    38. Henzy JE, Coffin JM. Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class. J Virol. 2013 Feb; 87(4):1937-46. PMID: 23221553; PMCID: PMC3571459.
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    39. Swanstrom R, Coffin J. HIV-1 pathogenesis: the virus. Cold Spring Harb Perspect Med. 2012 Dec; 2(12):a007443. PMID: 23143844.
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    40. Alter HJ, Mikovits JA, Switzer WM, Ruscetti FW, Lo SC, Klimas N, Komaroff AL, Montoya JG, Bateman L, Levine S, Peterson D, Levin B, Hanson MR, Genfi A, Bhat M, Zheng H, Wang R, Li B, Hung GC, Lee LL, Sameroff S, Heneine W, Coffin J, Hornig M, Lipkin WI. 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. MBio. 2012; 3(5). PMID: 22991430; PMCID: PMC3448165.
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    41. Boltz VF, Ambrose Z, Kearney MF, Shao W, Kewalramani VN, Maldarelli F, Mellors JW, Coffin JM. 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. J Virol. 2012 Dec; 86(23):12525-30. PMID: 22933296; PMCID: PMC3497681.
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    42. Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, Parker DC, Anderson EM, Kearney MF, Strain MC, Richman DD, Hudgens MG, Bosch RJ, Coffin JM, Eron JJ, Hazuda DJ, Margolis DM. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature. 2012 Jul 26; 487(7408):482-5. PMID: 22837004; NIHMSID: NIHMS383721.
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    43. Delviks-Frankenberry K, Cingöz O, Coffin JM, Pathak VK. Recombinant origin, contamination, and de-discovery of XMRV. Curr Opin Virol. 2012 Aug; 2(4):499-507. PMID: 22818188; NIHMSID: NIHMS392289.
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    44. Sanchez-Martinez S, Aloia AL, Harvin D, Mirro J, Gorelick RJ, Jern P, Coffin JM, Rein A. Studies on the restriction of murine leukemia viruses by mouse APOBEC3. PLoS One. 2012; 7(5):e38190. PMID: 22666481; PMCID: PMC3362552.
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    45. Archin NM, Vaidya NK, Kuruc JD, Liberty AL, Wiegand A, Kearney MF, Cohen MS, Coffin JM, Bosch RJ, Gay CL, Eron JJ, Margolis DM, Perelson AS. Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc Natl Acad Sci U S A. 2012 Jun 12; 109(24):9523-8. PMID: 22645358; PMCID: PMC3386138.
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    46. Tipper CH, Cingöz O, Coffin JM. Mus spicilegus endogenous retrovirus HEMV uses murine sodium-dependent myo-inositol transporter 1 as a receptor. J Virol. 2012 Jun; 86(11):6341-4. PMID: 22457525; PMCID: PMC3372175.
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    47. Kearney MF, Spindler J, Wiegand A, Shao W, Anderson EM, Maldarelli F, Ruscetti FW, Mellors JW, Hughes SH, Le Grice SF, Coffin JM. Multiple sources of contamination in samples from patients reported to have XMRV infection. PLoS One. 2012; 7(2):e30889. PMID: 22363509; PMCID: PMC3282701.
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    48. Del Prete GQ, Kearney MF, Spindler J, Wiegand A, Chertova E, Roser JD, Estes JD, Hao XP, Trubey CM, Lara A, Lee K, Chaipan C, Bess JW, Nagashima K, Keele BF, Macallister R, Smedley J, Pathak VK, Kewalramani VN, Coffin JM, Lifson JD. Restricted replication of xenotropic murine leukemia virus-related virus in pigtailed macaques. J Virol. 2012 Mar; 86(6):3152-66. PMID: 22238316; PMCID: PMC3302341.
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    49. Spindler J, Hackett J, Qiu X, Wiegand A, Boltz VF, Swanson P, Bream JH, Jacobson LP, Li X, Rinaldo CR, Wolinsky SM, Coffin JM, Kearney MF, Mellors JW. Prevalence of XMRV nucleic acid and antibody in HIV-1-Infected men and in men at risk for HIV-1 Infection. Adv Virol. 2011; 2011:268214. PMID: 22282703; NIHMSID: NIHMS346493.
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    50. Gray ER, Illingworth CJ, Coffin JM, Stoye JP. Binding of more than one Tva800 molecule is required for ASLV-A entry. Retrovirology. 2011; 8:96. PMID: 22099981; PMCID: PMC3267798.
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    51. Kearney MF, Lee K, Bagni RK, Wiegand A, Spindler J, Maldarelli F, Pinto PA, Linehan WM, Vocke CD, Delviks-Frankenberry KA, Devere White RW, Del Prete GQ, Mellors JW, Lifson JD, Kewalramani VN, Pathak VK, Coffin JM, Le Grice SF. Nucleic Acid, Antibody, and Virus Culture Methods to Detect Xenotropic MLV-Related Virus in Human Blood Samples. Adv Virol. 2011; 2011:272193. PMID: 22312339; PMCID: PMC3265299.
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    52. Subramanian RP, Wildschutte JH, Russo C, Coffin JM. Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology. 2011; 8:90. PMID: 22067224; PMCID: PMC3228705.
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    53. Palmer S, Boltz VF, Chow JY, Martinson NA, McIntyre JA, Gray GE, Hopley MJ, Mayers D, Robinson P, Hall DB, Maldarelli F, Coffin JM, Mellors JW. Short-course Combivir after single-dose nevirapine reduces but does not eliminate the emergence of nevirapine resistance in women. Antivir Ther. 2012; 17(2):327-36. PMID: 22293443.
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    54. Palmer S, Josefsson L, Coffin JM. HIV reservoirs and the possibility of a cure for HIV infection. J Intern Med. 2011 Dec; 270(6):550-60. PMID: 21929712.
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    55. Cingöz O, Paprotka T, Delviks-Frankenberry KA, Wildt S, Hu WS, Pathak VK, Coffin JM. Characterization, mapping, and distribution of the two XMRV parental proviruses. J Virol. 2012 Jan; 86(1):328-38. PMID: 22031947; PMCID: PMC3255884.
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    56. Cingöz O, Coffin JM. Endogenous Murine Leukemia Viruses: Relationship to XMRV and Related Sequences Detected in Human DNA Samples. Adv Virol. 2011; 2011:940210. PMID: 22312358; PMCID: PMC3265319.
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    57. Mens H, Kearney M, Wiegand A, Spindler J, Maldarelli F, Mellors JW, Coffin JM. Amplifying and quantifying HIV-1 RNA in HIV infected individuals with viral loads below the limit of detection by standard clinical assays. J Vis Exp. 2011; (55). PMID: 21968801; PMCID: PMC3230205.
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    58. Simmons G, Glynn SA, Komaroff AL, Mikovits JA, Tobler LH, Hackett J, Tang N, Switzer WM, Heneine W, Hewlett IK, Zhao J, Lo SC, Alter HJ, Linnen JM, Gao K, Coffin JM, Kearney MF, Ruscetti FW, Pfost MA, Bethel J, Kleinman S, Holmberg JA, Busch MP. Failure to confirm XMRV/MLVs in the blood of patients with chronic fatigue syndrome: a multi-laboratory study. Science. 2011 Nov 11; 334(6057):814-7. PMID: 21940862; NIHMSID: NIHMS340924.
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    59. Josefsson L, King MS, Makitalo B, Brännström J, Shao W, Maldarelli F, Kearney MF, Hu WS, Chen J, Gaines H, Mellors JW, Albert J, Coffin JM, Palmer SE. Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule. Proc Natl Acad Sci U S A. 2011 Jul 5; 108(27):11199-204. PMID: 21690402; PMCID: PMC3131354.
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    60. Paprotka T, Delviks-Frankenberry KA, Cingöz O, Martinez A, Kung HJ, Tepper CG, Hu WS, Fivash MJ, Coffin JM, Pathak VK. Recombinant origin of the retrovirus XMRV. Science. 2011 Jul 1; 333(6038):97-101. PMID: 21628392; NIHMSID: NIHMS350457.
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    61. Boltz VF, Zheng Y, Lockman S, Hong F, Halvas EK, McIntyre J, Currier JS, Chibowa MC, Kanyama C, Nair A, Owino-Ong'or W, Hughes M, Coffin JM, Mellors JW. Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine. Proc Natl Acad Sci U S A. 2011 May 31; 108(22):9202-7. PMID: 21576473; PMCID: PMC3107269.
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    62. Batorsky R, Kearney MF, Palmer SE, Maldarelli F, Rouzine IM, Coffin JM. Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc Natl Acad Sci U S A. 2011 Apr 5; 108(14):5661-6. PMID: 21436045; PMCID: PMC3078368.
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    63. Anderson JA, Archin NM, Ince W, Parker D, Wiegand A, Coffin JM, Kuruc J, Eron J, Swanstrom R, Margolis DM. 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. J Virol. 2011 May; 85(10):5220-3. PMID: 21367910; PMCID: PMC3126162.
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    64. Simmons G, Glynn SA, Holmberg JA, Coffin JM, Hewlett IK, Lo SC, Mikovits JA, Switzer WM, Linnen JM, Busch MP. The Blood Xenotropic Murine Leukemia Virus-Related Virus Scientific Research Working Group: mission, progress, and plans. Transfusion. 2011 Mar; 51(3):643-53. PMID: 21366602; NIHMSID: NIHMS264467.
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    65. Robinson MJ, Erlwein OW, Kaye S, Weber J, Cingoz O, Patel A, Walker MM, Kim WJ, Uiprasertkul M, Coffin JM, McClure MO. Mouse DNA contamination in human tissue tested for XMRV. Retrovirology. 2010; 7:108. PMID: 21171966; PMCID: PMC3019155.
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    66. Oakes B, Tai AK, Cingöz O, Henefield MH, Levine S, Coffin JM, Huber BT. Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences. Retrovirology. 2010; 7:109. PMID: 21171973; PMCID: PMC3022687.
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    67. Kearney M, Spindler J, Shao W, Maldarelli F, Palmer S, Hu SL, Lifson JD, KewalRamani VN, Mellors JW, Coffin JM, Ambrose Z. Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy. J Virol. 2011 Jan; 85(2):1067-76. PMID: 21084490; PMCID: PMC3019993.
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    68. Mens H, Kearney M, Wiegand A, Shao W, Schønning K, Gerstoft J, Obel N, Maldarelli F, Mellors JW, Benfield T, Coffin JM. HIV-1 continues to replicate and evolve in patients with natural control of HIV infection. J Virol. 2010 Dec; 84(24):12971-81. PMID: 20926564; PMCID: PMC3004307.
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    69. Gandhi RT, Zheng L, Bosch RJ, Chan ES, Margolis DM, Read S, Kallungal B, Palmer S, Medvik K, Lederman MM, Alatrakchi N, Jacobson JM, Wiegand A, Kearney M, Coffin JM, Mellors JW, Eron JJ. The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial. PLoS Med. 2010; 7(8). PMID: 20711481; PMCID: PMC2919424.
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    70. Galli A, Kearney M, Nikolaitchik OA, Yu S, Chin MP, Maldarelli F, Coffin JM, Pathak VK, Hu WS. 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. J Virol. 2010 Aug; 84(15):7651-61. PMID: 20504919; PMCID: PMC2897624.
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    164. Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995 Jan 27; 267(5197):483-9. PMID: 7824947.
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    256. Coffin JM, Temin HM. Comparison of Rous sarcoma virus-specific deoxyribonucleic acid polymerases in virions of Rous sarcoma virus and in Rous sarcoma virus-infected chicken cells. J Virol. 1971 May; 7(5):625-34. PMID: 4326752; PMCID: PMC356172.
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