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Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults.

Kearney MF, Spindler J, Wiegand A, Shao W, Haubrich R, Riddler S, Lalama CM, Hughes MD, Coffin JM, Mellors JW.

PLoS One. 2018 Jan 25;13(1):e0190438. doi: 10.1371/journal.pone.0190438. eCollection 2018.


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

Montesion M, Bhardwaj N, Williams ZH, Kuperwasser C, Coffin JM.

J Virol. 2017 Dec 14;92(1). pii: e01258-17. doi: 10.1128/JVI.01258-17. Print 2018 Jan 1.


No evidence of HIV replication in children on antiretroviral therapy.

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.

J Clin Invest. 2017 Oct 2;127(10):3827-3834. doi: 10.1172/JCI94582. Epub 2017 Sep 11.


Immunogenicity of AGS-004 Dendritic Cell Therapy in Patients Treated During Acute HIV Infection.

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.

AIDS Res Hum Retroviruses. 2018 Jan;34(1):111-122. doi: 10.1089/aid.2017.0071. Epub 2017 Jun 21.


Clinical Trial of the Anti-PD-L1 Antibody BMS-936559 in HIV-1 Infected Participants on Suppressive Antiretroviral Therapy.

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; AIDS Clinical Trials 5326 Study Team.

J Infect Dis. 2017 Jun 1;215(11):1725-1733. doi: 10.1093/infdis/jix191.


Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART.

Wiegand A, Spindler J, Hong FF, Shao W, Cyktor JC, Cillo AR, Halvas EK, Coffin JM, Mellors JW, Kearney MF.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):E3659-E3668. doi: 10.1073/pnas.1617961114. Epub 2017 Apr 17.


Pushing the envelope.

Wildschutte JH, Coffin JM.

Elife. 2017 Apr 13;6. pii: e26397. doi: 10.7554/eLife.26397.


Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir.

Bui JK, Sobolewski MD, Keele BF, Spindler J, Musick A, Wiegand A, Luke BT, Shao W, Hughes SH, Coffin JM, Kearney MF, Mellors JW.

PLoS Pathog. 2017 Mar 22;13(3):e1006283. doi: 10.1371/journal.ppat.1006283. eCollection 2017 Mar.


Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

Boltz VF, Rausch J, Shao W, Hattori J, Luke B, Maldarelli F, Mellors JW, Kearney MF, Coffin JM.

Retrovirology. 2016 Dec 20;13(1):87. doi: 10.1186/s12977-016-0321-6.


The Discovery of Reverse Transcriptase.

Coffin JM, Fan H.

Annu Rev Virol. 2016 Sep 29;3(1):29-51. Epub 2016 Jul 22. Review.


Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

Shao W, Shan J, Kearney MF, Wu X, Maldarelli F, Mellors JW, Luke B, Coffin JM, Hughes SH.

Retrovirology. 2016 Jul 4;13(1):47. doi: 10.1186/s12977-016-0277-6.


What Integration Sites Tell Us about HIV Persistence.

Hughes SH, Coffin JM.

Cell Host Microbe. 2016 May 11;19(5):588-98. doi: 10.1016/j.chom.2016.04.010. Review.


Discovery of unfixed endogenous retrovirus insertions in diverse human populations.

Wildschutte JH, Williams ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2326-34. doi: 10.1073/pnas.1602336113. Epub 2016 Mar 21.


Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo.

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.

Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1883-8. doi: 10.1073/pnas.1522675113. Epub 2016 Feb 8.


The discovery of HTLV-1, the first pathogenic human retrovirus.

Coffin JM.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):15525-9. doi: 10.1073/pnas.1521629112.


Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy.

Kearney MF, Wiegand A, Shao W, Coffin JM, Mellors JW, Lederman M, Gandhi RT, Keele BF, Li JZ.

J Virol. 2015 Nov 18;90(3):1369-76. doi: 10.1128/JVI.02139-15. Print 2016 Feb 1.


Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy.

Kearney MF, Anderson EM, Coomer C, Smith L, Shao W, Johnson N, Kline C, Spindler J, Mellors JW, Coffin JM, Ambrose Z.

Retrovirology. 2015 Nov 11;12:93. doi: 10.1186/s12977-015-0212-2.


Differential expression of HERV-K (HML-2) proviruses in cells and virions of the teratocarcinoma cell line Tera-1.

Bhardwaj N, Montesion M, Roy F, Coffin JM.

Viruses. 2015 Mar 4;7(3):939-68. doi: 10.3390/v7030939.


RNA editing, epitranscriptomics, and processing in cancer progression.

Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Howcroft TK, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E.

Cancer Biol Ther. 2015;16(1):21-7. doi: 10.4161/15384047.2014.987555.


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.

Sheng-Fowler L, Tu W, Fu H, Murata H, Lanning L, Foseh G, Macauley J, Blair D, Hughes SH, Coffin JM, Lewis AM Jr, Peden K.

PLoS One. 2014 Oct 10;9(10):e108926. doi: 10.1371/journal.pone.0108926. eCollection 2014.


Improved single-copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy.

Cillo AR, Vagratian D, Bedison MA, Anderson EM, Kearney MF, Fyne E, Koontz D, Coffin JM, Piatak M Jr, Mellors JW.

J Clin Microbiol. 2014 Nov;52(11):3944-51. doi: 10.1128/JCM.02060-14. Epub 2014 Sep 3.


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

Wildschutte JH, Ram D, Subramanian R, Stevens VL, Coffin JM.

Retrovirology. 2014 Aug 12;11:62. doi: 10.1186/s12977-014-0062-3.


HIV-1 infection leads to increased transcription of human endogenous retrovirus HERV-K (HML-2) proviruses in vivo but not to increased virion production.

Bhardwaj N, Maldarelli F, Mellors J, Coffin JM.

J Virol. 2014 Oct;88(19):11108-20. doi: 10.1128/JVI.01623-14. Epub 2014 Jul 23.


HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells.

Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH.

Science. 2014 Jul 11;345(6193):179-83. doi: 10.1126/science.1254194. Epub 2014 Jun 26.


Quantification of HIV-1 latency reversal in resting CD4+ T cells from patients on suppressive antiretroviral therapy.

Cillo AR, Sobolewski MD, Bosch RJ, Fyne E, Piatak M Jr, Coffin JM, Mellors JW.

Proc Natl Acad Sci U S A. 2014 May 13;111(19):7078-83. doi: 10.1073/pnas.1402873111. Epub 2014 Mar 31.


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

Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM.

J Virol Methods. 2014 Jul;203:73-80. doi: 10.1016/j.jviromet.2014.03.008. Epub 2014 Mar 26.


Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy.

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.

PLoS Pathog. 2014 Mar 20;10(3):e1004010. doi: 10.1371/journal.ppat.1004010. eCollection 2014 Mar.


Endogenous retroviruses and human cancer: is there anything to the rumors?

Bhardwaj N, Coffin JM.

Cell Host Microbe. 2014 Mar 12;15(3):255-9. doi: 10.1016/j.chom.2014.02.013.


HIV-1 expression within resting CD4+ T cells after multiple doses of vorinostat.

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.

J Infect Dis. 2014 Sep 1;210(5):728-35. doi: 10.1093/infdis/jiu155. Epub 2014 Mar 11.


Fifteen years later: hard and soft selection sweeps confirm a large population number for HIV in vivo.

Rouzine IM, Coffin JM, Weinberger LS.

PLoS Genet. 2014 Feb 20;10(2):e1004179. doi: 10.1371/journal.pgen.1004179. eCollection 2014 Feb. No abstract available.


False-positive HIV PCR test following ex vivo lentiviral gene transfer treatment of X-linked severe combined immunodeficiency vector.

De Ravin SS, Gray JT, Throm RE, Spindler J, Kearney M, Wu X, Coffin JM, Hughes SH, Malderelli F, Sorrentino BP, Malech HL.

Mol Ther. 2014 Feb;22(2):244-245. doi: 10.1038/mt.2013.296. No abstract available.


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.

Boltz VF, Bao Y, Lockman S, Halvas EK, Kearney MF, McIntyre JA, Schooley RT, Hughes MD, Coffin JM, Mellors JW; OCTANE/A5208 Team.

J Infect Dis. 2014 Mar 1;209(5):703-10. doi: 10.1093/infdis/jit635. Epub 2014 Jan 16.


A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses.

Henzy JE, Gifford RJ, Johnson WE, Coffin JM.

J Virol. 2014 Mar;88(5):2398-405. doi: 10.1128/JVI.02863-13. Epub 2013 Dec 18.


Generation of multiple replication-competent retroviruses through recombination between PreXMRV-1 and PreXMRV-2.

Delviks-Frankenberry K, Paprotka T, Cingöz O, Wildt S, Hu WS, Coffin JM, Pathak VK.

J Virol. 2013 Nov;87(21):11525-37. doi: 10.1128/JVI.01787-13. Epub 2013 Aug 21.


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.

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.

PLoS Pathog. 2013;9(6):e1003432. doi: 10.1371/journal.ppat.1003432. Epub 2013 Jun 20.


Virions at the gates: receptors and the host-virus arms race.

Coffin JM.

PLoS Biol. 2013;11(5):e1001574. doi: 10.1371/journal.pbio.1001574. Epub 2013 May 28.


HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.

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.

J Virol. 2013 Sep;87(18):10313-23. doi: 10.1128/JVI.01225-12. Epub 2013 May 15.


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

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.


Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class.

Henzy JE, Coffin JM.

J Virol. 2013 Feb;87(4):1937-46. doi: 10.1128/JVI.01442-12. Epub 2012 Dec 5.


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.

Boltz VF, Ambrose Z, Kearney MF, Shao W, Kewalramani VN, Maldarelli F, Mellors JW, Coffin JM.

J Virol. 2012 Dec;86(23):12525-30. doi: 10.1128/JVI.01963-12. Epub 2012 Aug 29.


Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy.

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.

Nature. 2012 Jul 25;487(7408):482-5. doi: 10.1038/nature11286. Erratum in: Nature. 2012 Sep 20;489(7416):460.


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

Delviks-Frankenberry K, Cingöz O, Coffin JM, Pathak VK.

Curr Opin Virol. 2012 Aug;2(4):499-507. doi: 10.1016/j.coviro.2012.06.009. Epub 2012 Jul 19. Review.


Studies on the restriction of murine leukemia viruses by mouse APOBEC3.

Sanchez-Martinez S, Aloia AL, Harvin D, Mirro J, Gorelick RJ, Jern P, Coffin JM, Rein A.

PLoS One. 2012;7(5):e38190. doi: 10.1371/journal.pone.0038190. Epub 2012 May 29.


Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection.

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.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9523-8. doi: 10.1073/pnas.1120248109. Epub 2012 May 29.


Mus spicilegus endogenous retrovirus HEMV uses murine sodium-dependent myo-inositol transporter 1 as a receptor.

Tipper CH, Cingöz O, Coffin JM.

J Virol. 2012 Jun;86(11):6341-4. doi: 10.1128/JVI.00083-12. Epub 2012 Mar 28.


Multiple sources of contamination in samples from patients reported to have XMRV infection.

Kearney MF, Spindler J, Wiegand A, Shao W, Anderson EM, Maldarelli F, Ruscetti FW, Mellors JW, Hughes SH, Le Grice SF, Coffin JM.

PLoS One. 2012;7(2):e30889. doi: 10.1371/journal.pone.0030889. Epub 2012 Feb 20.


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

Cingöz O, Coffin JM.

Adv Virol. 2011;2011:940210. doi: 10.1155/2011/940210. Epub 2011 Oct 24.


Nucleic Acid, Antibody, and Virus Culture Methods to Detect Xenotropic MLV-Related Virus in Human Blood Samples.

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.

Adv Virol. 2011;2011:272193. doi: 10.1155/2011/272193. Epub 2011 Nov 17.


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

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; 1100.1413 Trial Investigators.

Antivir Ther. 2012;17(2):327-36. doi: 10.3851/IMP1946. Epub 2011 Nov 3.


Prevalence of XMRV nucleic acid and antibody in HIV-1-Infected men and in men at risk for HIV-1 Infection.

Spindler J, Hackett J Jr, Qiu X, Wiegand A, Boltz VF, Swanson P, Bream JH, Jacobson LP, Li X, Rinaldo CR, Wolinsky SM, Coffin JM, Kearney MF, Mellors JW.

Adv Virol. 2011;2011:268214. doi: 10.1155/2011/268214. Epub 2011 Nov 21.

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