Replication, Population Dynamics, Genetics, & Evolution of Retroviruses



Principal Investigator
John Coffin
ACS Research Professor

Program Affiliations
Genetics
Molecular Microbiology

Contact Information
Department of Microbiology
Tufts University
136 Harrison Avenue
Boston, MA 02111

Office (617) 636-6528
Lab (617) 636-0918
Fax (617) 636-0337
Email  
John.Coffin@tufts.edu
  1. Hughes, J.F. and Coffin, J.M., 2004.  HERV-K solo LTR formation and insertional polymorphisms:  Implications for human evolution. PNAS 101: 1668-1672.
  2. Maxfield, L., Fraize, C.D., and Coffin, J.M. 2005. Relationship Between Retroviral DNA Integration Site Selection and Host Cell Transcription. PNAS 102: 1436-1441.
  3. Rouzine, I.M. and Coffin, J.M. 2005. Evolution of HIV under selection and weak recombination. Genetics 170: 7-18.
  4. Tipper, C.H. Bencsics, C.E., and Coffin, J.M. 2005. Characterization of HEMV, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup.  J. Virol. 79: 8316-8329.
  5. 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.
  6. Holman, A. and Coffin, J.M. 2005. Symmetrical base preferences surrounding HIV-1, ASLV, and MLV integration sites.  PNAS 102: 6103-6107.
  7. Rainey, G.J. and Coffin, J.M. 2006. Evolution of broad host range in retroviruses leads to apoptosis mediated by highly cytopathic variants.  J. Virol. 80: 562-570.
  8. Palmer, S., Boltz, V., Maldarelli, F., Kearney, M., Halvas, E.K., Rock, D., Falloon.J., Davey, T.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.
  9. 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 for prevention of maternal to fetal transmission. PNAS 103: 7094-7099.
  10. Gheorghiu-Svirschevski, S., Coffin, J.M., and Rouzine, I. M. 2007. Increasing sequence correlation limits the efficiency of recombination in a multi-site evolution model. Mol. Biol. Evol. 24:574-586.
  11. 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., Mellors, J.W. 2007. Suppressive antiretroviral therapy lowers plasma HIV-1 RNA to stable set-point predicted by pretreatment viremia but not treatment regimen. PloS Pathog 3: e46.
  12. Rouzine, I.M., and Coffin, J.M. 2007. Highly fit ancestors of a partly sexual haploid population. Theor Pop. Biol. 71 239-250.
  13. 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 AZT resistance. PNAS 104: 317-322.
  14. Ambrose, Z., Palmer, S., Boltz, V.F., Kearney, M., Larsen, K., Polacino, P., Flanary, L., Oswald, K., Piatak, Jr., M., 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.
  15. Jern P, Stoye, JP, and Coffin, JM.  2007. Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses. PLoS Genet. 3:2014-2022.
  16. Sheng L, Cai F, Zhu Y, Pal A, Athanasiou M, Orrison B, Blair DG, Hughes SH, Coffin J, Lewis AM, and Peden K: 2008. Oncogenicity of DNA in vivo:  Tumor induction with expression plasmids for activated H-ras and cy-myc. Biologicals. 36: 184-197.
  17. Palmer S, Maldarelli F, Wiegand A, Bernstein B, Hanna GJ, Brun SC, Kempf DJ, Mellors JW, Coffin JM, and King MS. 2008. Low-level viremia persists for at least seven years in patients on suppressive antiretroviral therapy. PNAS. 105: 3879-3884.
  18. Rulli SJ Jr, Mirro J, Hill SA, Lloyd P, Gorelick RJ, Coffin JM, Derse D, Rein A. 2008. Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses. J. Virol. 85:6566-6575.
  19. Delviks-Frankenberry KA, Nikolenko GN, Boyer PL, Hughes SH, Coffin JM, Jere A, and Pathak V. 2008. HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision. Proc. Natl. Acad. Sci. USA, In Press.
  20. Jern, P and Coffin, J.M.  2008. Effect of retroviruses on host genome function. Ann. Rev. Gen. 42: 20.1-20.23.