Selected Publications

Delviks-Frankenberry, K.A., Nikolenko, G.N., Boyer, P.L., Hughes, S.H., Coffin, J.M., Jere, A., and Pathak, V.K.  (2008)  HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.  Proc. Natl. Acad. Sci. USA, in press.

Archin, N.M., Eron, J.J., Palmer, S., Hartmann-Duff, A., Martinson, J.A., Wiegand, A., Bandarenko, N., Schmitz, J.L., Bosch, R.J., Landay, A.L., Coffin, J.M., and Margolis, D.M.  (2008)  Valproic acid without intensified antiviral therapy has limited impact on persistent HIV infection of resting CD4+ T cells.  AIDS 22: 1131-1135.
[Abstract]     [Full-text PDF article]

Rulli, S.J., Jr., Mirro, J., Hill, S.A., Lloyd, P., Gorelick, R.J., Coffin, J.M., Derse, D., and Rein, A.  (2008)  Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses.  J. Virol. 82: 6566-6575.
[Abstract]     [Full-text PDF article]

Palmer, S., Maldarelli, F., Wiegand, A., Bernstein, B., Hanna, G.J., Brun, S.C., Kempf, D.J., Mellors, J.W., Coffin, J.M., and King, M.S.  (2008)  Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy.  Proc. Natl. Acad. Sci. USA 105: 3879-3884.     [Abstract]     [Full-text PDF article]

Kearney, M., Palmer, S., Maldarelli, F., Shao, W., Polis, M.A., Mican, J., Rock-Kress, D., Margolick, J.B., Coffin, J.M., and Mellors, J.W.  (2008)  Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase.  AIDS 22: 497-501.
[Abstract]     [Full-text PDF article]

Sheng, L., Cai, F., Zhu, Y., Pal, A., Athanasiou, M., Orrison, B., Blair, D.G., Hughes, S.H., Coffin, J.M., Lewis, A.M., and Peden, K.  (2008)  Oncogenicity of DNA in vivo: Tumor induction with expression plasmids for activated H-ras and c-myc.  Biologicals 36: 184-197.     [Abstract]     [Full-text PDF article]

Jern, P., Stoye, J.P., and Coffin, J.M.  (2007)  Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses.  PLoS Genet. 3: 2014-2022.
[Abstract]     [Full-text PDF article]

Kaufmann, D.E., Kavanagh, D.G., Pereyra, F., Zaunders, J.J., Mackey, E.W., Miura, T., Palmer, S., Brockman, M., Rathod, A., Piechocka-Trocha, A., Baker, B., Zhu, B., Le Gall, S., Waring, M.T., Ahern, R., Moss, K., Kelleher, A.D., Coffin, J.M., Freeman, G.J., Rosenberg, E.S., and Walker, B.D.  (2007)  Upregulation of CTLA-4 by HIV-specific CD4(+) T cells correlates with disease progression and defines a reversible immune dysfunction.  Nat. Immunol. 8: 1246-1254.     [Abstract]     [Full-text PDF article]

Ambrose, Z., Palmer, S., Boltz, V.F., Kearney, M., Larsen, K., Polacino, P., Flanary, L., Oswald, K., Piatak, M., Jr., Smedley, J., Shao, W., Bischofberger, N., Maldarelli, F., Kimata, J.T., Mellors, J.W., Hu, S.-L., Coffin, J.M., Lifson, J.D., and KewalRamani, V.N.  (2007)  Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy.  J. Virol. 81: 12145-12155.
[Abstract]     [Full-text PDF article]

Maldarelli, F., Palmer, S., King, M.S., Wiegand, A., Polis, M.A., Mican, J., Kovacs, J.A., Davey, R.T., Rock-Kress, D., Dewar, R., Liu, S., Metcalf, J.A., Rehm, C., Brun, S.C., Hanna, G.J., Kempf, D.J., Coffin, J.M., and Mellors, J.W.  (2007)  ART suppresses plasma HIV- 1 RNA to a stable set point predicted by pretherapy viremia.  PLoS Pathog. 3: e46.
[Abstract]     [Full-text PDF article]

Nikolenko, G.N., Delviks-Frankenberry, K.A., Palmer, S., Maldarelli, F., Fivash, M.J., Jr., Coffin, J.M., and Pathak, V.K.  (2007)  Mutations in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine resistance.  Proc. Natl. Acad. Sci. USA 104: 317-322.      [Abstract]     [Full-text PDF article]

Gheorghiu-Svirschevski, S., Rouzine, I.M., and Coffin, J.M.  (2007)  Increasing sequence correlation limits the efficiency of recombination in a multisite evolution model.  Mol. Biol. Evol. 24: 574-586.     [Abstract]      [Full-text PDF article]

Rouzine, I.M., and Coffin, J.M.  (2007)  Highly fit ancestors of a partly sexual haploid population.  Theor. Popul. Biol. 71: 239-250.     [Abstract]      [Full-text PDF article]

Halvas, E.K., Aldrovandi, G.M., Balfe, P., Beck, I.A., Boltz, V.F., Coffin, J.M., Frenkel, L.M., Hazelwood, J.D., Johnson, V.A., Kearney, M., Kovacs, A., Kuritzkes, D.R., Metzner, K.J., Nissley, D.V., Nowicki, M., Palmer, S., Ziermann, R., Zhao, R.Y., Jennings, C.L., Bremer, J., Brambilla, D., and Mellors, J.W.  (2006)  Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency.   J. Clin. Microbiol. 44: 2612-2614.     [Abstract]      [Full-text PDF article]

Palmer, S., Boltz, V., Martinson, N., Maldarelli, F., Gray, G., McIntyre, J., Mellors, J., Morris, L., and Coffin, J.  (2006)  Persistence of nevirapine-resistant HIV-1 in women after single-dose nevirapine therapy for prevention of maternal-to-fetal HIV-1 transmission.  Proc. Natl. Acad. Sci. USA 103: 7094-7099.     [Abstract]     [Full-text PDF article]

Palmer, S., Boltz, V., Maldarelli, F., Kearney, M., Halvas, E.K., Rock, D., Falloon, J., Davey, R.T., Jr., Dewar, R.L., Metcalf, J.A., Mellors, J.W., and Coffin, J.M.  (2006)  Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.  AIDS 20: 701-710.
[Abstract]     [Full-text PDF article]

Rainey, G.J.A., and Coffin, J.M.  (2006)  Evolution of broad host range in retroviruses leads to cell death mediated by highly cytopathic variants.  J. Virol. 80: 562-570.
[Abstract]     [Full-text PDF article]

Hughes, J.F., and Coffin, J.M.  (2005)  Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome.  Genetics 171: 1183-1194.
[Abstract]     [Full-text PDF article]

Lehrman, G., Hogue, I.B., Palmer, S., Jennings, C., Spina, C.A., Wiegand, A., Landay, A.L., Coombs, R.W., Richman, D.D., Mellors, J.W., Coffin, J.M., Bosch, R.J., and Margolis, D.M.  (2005)  Depletion of latent HIV-1 infection in vivo: A proof-of-concept study.  Lancet 366: 549-555.     [Abstract]     [Full-text PDF article]

Tipper, C.H., Bencsics, C.E., and Coffin, J.M.  (2005)  Characterization of hortulanus endogenous murine leukemia virus, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup.  J. Virol. 79: 8316-8329.
[Abstract]     [Full-text PDF article]

Rouzine, I.M., and Coffin, J.M.  (2005)  Evolution of human immunodeficiency virus under selection and weak recombination.  Genetics 170: 7-18.     [Abstract]     [Full-text PDF article]

Holman, A.G., and Coffin, J.M..  (2005)  Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites.  Proc. Natl. Acad. Sci. USA 102: 6103-6107.     [Abstract]     [Full-text PDF article]

Nikolenko, G.N., Palmer, S., Maldarelli, F., Mellors, J.W., Coffin, J.M., and Pathak, V.K.  (2005)  Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: Balance between RNase H activity and nucleotide excision.  Proc. Natl. Acad. Sci. USA 102: 2093-2098.     [Abstract]     [Full-text PDF article]

Maxfield, L.F., Fraize, C.D., and Coffin, J.M.  (2005)  Relationship between retroviral DNA-integration-site selection and host cell transcription.  Proc. Natl. Acad. Sci. USA 102: 1436-1441.     [Abstract]     [Full-text PDF article]

Palmer, S., Kearney, M., Maldarelli, F., Halvas, E.K., Bixby, C.J., Bazmi, H., Rock, D., Falloon, J., Davey, R.T., Jr., Dewar, R.L., Metcalf, J.A., Hammer, S., Mellors, J.W., and Coffin, J.M.  (2005)  Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis.  J. Clin. Microbiol. 43: 406-413.      [Abstract]     [Full-text PDF article]

Ambrose, Z., Boltz, V., Palmer, S., Coffin, J.M., Hughes, S.H., and KewalRamani, V.N.  (2004)  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.  J. Virol. 78: 13553-13561.
[Abstract]     [Full-text PDF article]

Achaz, G., Palmer, S., Kearney, M., Maldarelli, F., Mellors, J.W., Coffin, J.M., and Wakeley, J.  (2004)  A robust measure of HIV-1 population turnover within chronically infected individuals.  Mol. Biol. Evol. 21: 1902-1912.     [Abstract]     [Full-text PDF article]

Coffin, J.M.  (2004)  Evolution of retroviruses:  Fossils in our DNA.  Proc. Am. Philos. Soc. 148: 264-280.     [PubMed citation]

Dybul, M., Nies-Kraske, E., Dewar, R., Maldarelli, F., Hallahan, C.W., Daucher, M., Piscitelli, S.C., Ehler, L., Weigand, A., Palmer, S., Metcalf, J.A., Davey, R.T., Rock Kress, D.M., Powers, A., Beck, I., Frenkel, L., Baseler, M., Coffin, J., and Fauci, A.S.  (2004)  A proof-of-concept study of short-cycle intermittent antiretroviral therapy with a once-daily regimen of didanosine, lamivudine, and efavirenz for the treatment of chronic HIV infection.  J. Infect. Dis. 189: 1974-1982.     [Abstract]     [Full-text PDF article]

Yu, Q., Konig, R., Pillai, S., Chiles, K., Kearney, M., Palmer, S., Richman, D., Coffin, J.M., and Landau, N.R.  (2004)  Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome.  Nat. Struct. Mol. Biol. 11: 435-442.
[Abstract]     [Full-text PDF article]

Hughes, J.F., and Coffin, J.M.  (2004)  Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: Implications for human and viral evolution.  Proc. Natl. Acad. Sci. USA 101:1668-16721.      [Abstract]     [Full-text PDF article]

Dang, Q., Chen, J., Unutmaz, D., Coffin, J.M., Pathak, V.K., Powell, D., KewalRamani, V.N., Maldarelli, F., and Hu, W.-S.  (2004)  Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways.  Proc. Natl. Acad. Sci. USA 101: 632-637.
[Abstract]     [Full-text PDF article]     [Supporting text]

Palmer, S., Wiegand, A.P., Maldarelli, F., Bazmi, H., Mican, J.M., Polis, M., Dewar, R.L., Planta, A., Liu, S., Metcalf, J.A., Mellors, J.W., and Coffin, J.M.  (2003)  New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma.  J. Clin. Microbiol. 41: 4531-4536.
[Abstract]     [Full-text PDF article]

KewalRamani, V.N., and Coffin, J.M.  (2003)  Weapons of mutational destruction.  Science 301: 923-925.      [Summary]     [Full-text PDF article]

Rainey, G.J.A., Natonson, A., Maxfield, L.F., and Coffin, J.M.  (2003)  Mechanisms of avian retroviral host range extension.  J. Virol. 77: 6709-6719.
[Abstract]     [Full-text PDF article]

Rouzine, I.M., Wakeley, J., and Coffin, J.M.  (2003)  The solitary wave of asexual evolution.  Proc. Natl. Acad. Sci. USA 100: 587-592.      [Abstract]     [Full-text PDF article]
[Mathematical Appendix]

Palmer, S., Kearney, M., Maldarelli, F., Kottilil, S., Lucey, D., Metcalf, J., Rock, D., VanHoutte, M., Michels, L., Hertogs, K., Mellors, J., and Coffin, J.  (2002)  Genetics of HIV-1 populations in acute and chronic infection.  Antiviral Ther. 7: S57.

Hughes, J.F., and Coffin, J.M. (2002) A novel endogenous retrovirus-related element in the human genome resembles a DNA transposon: evidence for an evolutionary link? Genomics 80:453-455.
[Abstract]     [Full-text PDF article]

Hughes, J.F., and Coffin, J.M. (2001) Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution. Nat. Genet. 29: 487-489.
[Abstract]     [Full-text PDF article]

Rouzine, I.M., Rodrigo, A., and Coffin, J.M. (2001) Transition between stochastic evolution and deterministic evolution in the presence of selection: General theory and application to virology. Microbiol. Mol. Biol. Rev. 65:151-185.
[Abstract]     [Full-text PDF article]

Zhou, H., Rainey, G.J., Wong, S.-K., and Coffin, J.M. (2001) Substrate sequence selection by retroviral integrase. J. Virol. 75: 1359-1370.
[Abstract]     [Full-text PDF article]

Weidhaas, J.B., Angelichio, E.L., Fenner, S., and Coffin, J.M. (2000) Relationship between retroviral DNA integration and gene expression. J. Virol. 74: 8382-8389.
[Abstract]     [Full-text PDF article]

Rouzine, I.M., and Coffin, J.M. (1999) Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proc. Natl. Acad. Sci. USA 96: 10758-10763.
[Abstract]     [Full-text PDF article]

Rouzine, I.M., and Coffin, J.M. (1999) Search for the mechanism of genetic variation in the pro gene of human immunodeficiency virus. J. Virol. 73: 8167-8178.
[Abstract]     [Full-text PDF article]

Aschoff, J.M., Foster, D., and Coffin, J.M. (1999) Point mutations in the avian sarcoma/leukosis virus 3' untranslated region result in a packaging defect. J. Virol. 73: 7421-7429.
[Abstract]     [Full-text PDF article]

Johnson, W.E., and Coffin, J.M. (1999) Constructing primate phylogenies from ancient retrovirus sequences. Proc. Natl. Acad. Sci. USA 96: 10254-10260.      [Abstract]      [Full-text PDF article]

Tomonaga, K., and Coffin, J.M. (1999) Structures of endogenous nonecotropic murine leukemia virus (MLV) long terminal repeats in wild mice: implication for evolution of MLVs. J. Virol. 73: 4327-4340.      [Abstract]     [Full-text PDF article]

Rouzine, I.M., and Coffin, J.M. (1999) Technical Comments. T cell turnover in SIV infection.  Science 284: 555b.      [Full-text PDF article*^,§]

Coffin, J.M., Hughes, S.H., and Varmus, H.E. (eds.). (1997) Retroviruses. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.      [Link to Retroviruses at the National Center for Biotechnology Information website]     [For more information, go to the Cold Spring Harbor Laboratory Press website.]

Coffin, J.M. (1995) HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy. Science 267: 483-488.
[Abstract]     [Full-text PDF article^¶,§]

Withers-Ward, E.S., Kitamura, Y., Barnes, J.P., and Coffin, J.M. (1994) Distribution of targets for avian retrovirus DNA integration in vivo. Genes Dev. 8: 1473-1487.
[Abstract]

* Reprinted with permission from Science, 1999, Volume 284, pages 555a-555d.
© 1999 American Association for the Advancement of Science.

^¶ Reprinted with permission from Science, 1995, Volume 267, pages 483-488.
© 1995 American Association for the Advancement of Science.

^§ "Readers may view, browse, and/or download this material for temporary copying purposes only, provided these uses are for noncommercial personal purposes. Except as provided by law, this material may not be further reproduced, distributed, transmitted, modified, adapted, performed, displayed, published, or sold in whole or in part, without prior written permission from the Amercian Association for the Advancement of Science."