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An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses.

Wells DW, Guo S, Shao W, Bale MJ, Coffin JM, Hughes SH, Wu X.

BMC Genomics. 2020 Mar 9;21(1):216. doi: 10.1186/s12864-020-6647-4.


Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections.

Anderson EM, Simonetti FR, Gorelick RJ, Hill S, Gouzoulis MA, Bell J, Rehm C, Pérez L, Boritz E, Wu X, Wells D, Hughes SH, Rao V, Coffin JM, Kearney MF, Maldarelli F.

Viruses. 2020 Jan 25;12(2). pii: E136. doi: 10.3390/v12020136.


Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors.

Patro SC, Brandt LD, Bale MJ, Halvas EK, Joseph KW, Shao W, Wu X, Guo S, Murrell B, Wiegand A, Spindler J, Raley C, Hautman C, Sobolewski M, Fennessey CM, Hu WS, Luke B, Hasson JM, Niyongabo A, Capoferri AA, Keele BF, Milush J, Hoh R, Deeks SG, Maldarelli F, Hughes SH, Coffin JM, Rausch JW, Mellors JW, Kearney MF.

Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):25891-25899. doi: 10.1073/pnas.1910334116. Epub 2019 Nov 27.


HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus.

Musick A, Spindler J, Boritz E, Pérez L, Crespo-Vélez D, Patro SC, Sobolewski MD, Bale MJ, Reid C, Keele BF, Capoferri A, Shao W, Wiegand A, Simonetti FR, Mellors JW, Hughes SH, Coffin JM, Maldarelli F, Kearney MF.

Front Microbiol. 2019 Oct 1;10:2204. doi: 10.3389/fmicb.2019.02204. eCollection 2019.


HIV Proviral Sequence Database: A New Public Database for Near Full-Length HIV Proviral Sequences and Their Meta-Analyses.

Shao W, Shan J, Hu WS, Halvas EK, Mellors JW, Coffin JM, Kearney MF.

AIDS Res Hum Retroviruses. 2020 Jan;36(1):1-3. doi: 10.1089/AID.2019.0214. Epub 2019 Oct 29. No abstract available.


Linked dual-class HIV resistance mutations are associated with treatment failure.

Boltz VF, Shao W, Bale MJ, Halvas EK, Luke B, McIntyre JA, Schooley RT, Lockman S, Currier JS, Sawe F, Hogg E, Hughes MD, Kearney MF, Coffin JM, Mellors JW.

JCI Insight. 2019 Oct 3;4(19). pii: 130118. doi: 10.1172/jci.insight.130118.


HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy.

McManus WR, Bale MJ, Spindler J, Wiegand A, Musick A, Patro SC, Sobolewski MD, Musick VK, Anderson EM, Cyktor JC, Halvas EK, Shao W, Wells D, Wu X, Keele BF, Milush JM, Hoh R, Mellors JW, Hughes SH, Deeks SG, Coffin JM, Kearney MF.

J Clin Invest. 2019 Jul 30;130:4629-4642. doi: 10.1172/JCI126714.


Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans.

Ferris AL, Wells DW, Guo S, Del Prete GQ, Swanstrom AE, Coffin JM, Wu X, Lifson JD, Hughes SH.

PLoS Pathog. 2019 Jul 10;15(7):e1007869. doi: 10.1371/journal.ppat.1007869. eCollection 2019 Jul.


Clones of infected cells arise early in HIV-infected individuals.

Coffin JM, Wells DW, Zerbato JM, Kuruc JD, Guo S, Luke BT, Eron JJ, Bale M, Spindler J, Simonetti FR, Hill S, Kearney MF, Maldarelli F, Wu X, Mellors JW, Hughes SH.

JCI Insight. 2019 Jun 20;4(12). pii: 128432. doi: 10.1172/jci.insight.128432. eCollection 2019 Jun 20.


Retrospective Comparison of the Supported and Unsupported Bovine Jugular Vein Conduit in Children.

Lueth ET, Gist KM, Burkett DA, Landeck BF, Brinton JT, Meier MR, Coffin JM, Schafer M, Jaggers J, Mitchell MB.

Ann Thorac Surg. 2019 Aug;108(2):567-573. doi: 10.1016/j.athoracsur.2019.03.021. Epub 2019 Apr 8.


Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees.

Holloway JR, Williams ZH, Freeman MM, Bulow U, Coffin JM.

Proc Natl Acad Sci U S A. 2019 Jan 22;116(4):1337-1346. doi: 10.1073/pnas.1814203116. Epub 2019 Jan 4.


Ongoing HIV Replication During ART Reconsidered.

Kearney MF, Wiegand A, Shao W, McManus WR, Bale MJ, Luke B, Maldarelli F, Mellors JW, Coffin JM.

Open Forum Infect Dis. 2017 Sep 19;4(3):ofx173. doi: 10.1093/ofid/ofx173. eCollection 2017 Summer.


Nomenclature for endogenous retrovirus (ERV) loci.

Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE.

Retrovirology. 2018 Aug 28;15(1):59. doi: 10.1186/s12977-018-0442-1. Review.


Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites.

Montesion M, Williams ZH, Subramanian RP, Kuperwasser C, Coffin JM.

Retrovirology. 2018 Aug 20;15(1):57. doi: 10.1186/s12977-018-0441-2.


Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses.

Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski NE, Pappu HR, Pooggin MM, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH.

J Virol. 2018 May 29;92(12). pii: e00515-18. doi: 10.1128/JVI.00515-18. Print 2018 Jun 15. No abstract available.


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.

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