Principal Investigator
John Coffin
ACS Research Professor
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Program Affiliations
Genetics
Molecular Microbiology
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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
Send Email |
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Selected Publications
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
HIV-1drug resistance mutations in treatment-experienced
patients are missed by standard genotype analysis. J.
Clin. Microbiol. 43: 406-413.
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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.
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Rouzine, I.M. and Coffin, J.M. Evolution
of HIV under selection and weak recombination. 2005.
Genetics 170: 7-18.
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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.
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Hughes, J.F. and Coffin, J.M. 2005.
Human endogenous retroviral elements as indicators of
ectopic recombination events in the primate genome. Genetics
In Press
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Holman, A. and Coffin, J.M. 2005.
Symmetrical base preferences surrounding HIV-1, ASLV,
and MLV integration sites. PNAS 102: 6103-6107.
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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., Margolis, D.M. 2005. Depletion of latent
HIV-1 infection in vivo: a proof-of-concept study. Lancet
366:549-555.
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Achaz, G., Palmer, S., Kearney, M.,
Maldarelli, F., Mellors, J., Coffin, J., Wakeley, J.,
2004. Slow turnover of HIV-1 populations in chronically
infected individuals. Mol. Biol. Evol. 21:1902-1912.
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Dybul, M., E. Nies-Kraske, R. Dewar,
F. Maldarelli, A. Weigand, S. Palmer, C. W. Hallahan,
M. Daucher, S. C. Piscitelli, L. Ehler, J. A. Metcalf,
R. T. Davey, D. M. Rock Kress, A. Powers, I. Beck, L.
Frenkel, M. Baseler, J. Coffin and A. S. Fauci. 2004.
A proof-of-concept study of short cycle intermittent
antiretroviral therapy with a once per day regimen of
didanosine, lamivudine and efavirenz for the treatment
of chronic HIV infection. Journal of Infectious Diseases.
189: 1974-1982.
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Ambrose, Z., Boltz, V., Palmer, S.,
Coffin, J.M., Hughes, S.H., and KewalRamani, V.N. 2004.
In Vitro characterization of an SIV/HIV chimeric virus
expressing HIV-1 reverse transcriptase (RT-SHIV) to study
antiviral resistance in pigtail macaques. J. Virol. 78:
13553–13561.
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Nikolenko, G,N.Sarah Palmer, S. Frank
Maldarelli, F. Mellors, J.W., Coffin, J.M. and Pathak,
V.K. 2004. A novel mechanism for nucleoside analog-mediated
abrogation of HIV-1 replication: equilibrium between
RNase H activity and nucleotide excision. PNAS. 102:
2093-2098
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Coffin, J.M. 2004. Evolution of
retroviruses: Fossils in our DNA. Proc. Am. Phil. Soc.
148: 264-280.
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Yu Q., R. Konig, S. Pillai, K. Chiles,
M. Kearney, S. Palmer, D. Richman, J.M. Coffin and
N.R. Landau. 2004. Single-strand specificity of APOBEC3G
accounts for minus-strand deamination of the HIV genome.
Nat Struct Mol Biol. 11:435-42. Epub
2004 Apr 18.
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Dang Q., J. Chen, D. Unutmaz, J.M.
Coffin, V.K. Pathak, D. Powell, V.N. KewalRamani,
F. Maldarelli and W.S. Hu. 2004. Nonrandom HIV-1 infection
and double infection via direct and cell-mediated pathways.
Proc Natl Acad Sci U S A. 101:632-7.
Epub 2004 Jan 05.
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Hughes, J.F. and Coffin, J.M.,
2004. HERV-K solo LTR formation and insertional polymorphisms:
Implications for human evolution. PNAS 101:
1668-1672.
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KewalRamani, V.N., and Coffin,
J.M. 2003 Virology: Weapons of Mutational
destruction Science 301: 923-925.
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Palmer, S.E.,Wiegand, A.P., Maldarelli,
F. Bazmi, H., Mican, H., Mellors, J.W., and Coffin,
J.M. 2003. New real-time PCR assay quantifies
plasma HIV-1 RNA from 106 to 1 copy/ml. J.
Clin. Microbiol. 10: 4531-4536.
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Palmer S., A.P. Wiegand, F. Maldarelli,
H. Bazmi, J.M. Mican, M. Polis, R.L. Dewar, A. Planta,
S. Liu, J.A. Metcalf, J.W. Mellors and J.M. Coffin.
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. 41:4531-6.
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KewalRamani V.N. and J.M.
Coffin. 2003. Virology. Weapons of mutational
destruction. Science. 301:923-5.
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Rainey G.J., A. Natonson, L.F. Maxfield
and J.M. Coffin. 2003. Mechanisms of
avian retroviral host range extension. J Virol. 77:6709-19.
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Rouzine, I.M., Wakely, J., and Coffin,
J.M. 2003. The solitary wave of asexual evolution.
Proc. Natl. Acad. Sci. USA 100: 587-592.
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Hughes, J. and Coffin, J.M. 2002.
Novel endogenous retrovirus-related element in the human
genome resembles a DNA transposon: evidence for an evolutionary
link? Genomics. 80: 453-455.
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Hughes, J. and Coffin, J.M. 2001.
Evidence for human endogenous retrovirus-mediated genomic
rearrangements during primate evolution. Nat. Gen. 29:
487-489. PubMed
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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. PubMed
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Zhou, H., Rainey, G.J., Wong, S.K.,
and Coffin, J.M. 2001. Substrate sequence
selection by retroviral integrase. J. Virol. 75:
1359-1370. PubMed
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Stoye, J.P., and Coffin, J.M. 2000.
News and Views. Developmental biology: A provirus put
to work. Nature 403: 715 - 717
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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. PubMed
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Rouzine, I., and Coffin, J.M. 1999
Interplay between experiment and theory in development
of a working model for HIV-1 population dynamics. Chapter
10 in Origin and Evolution of Viruses (E. Domingo,
R. Webster, and J. Holland, eds) pp 225-262.
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Reuss, F.U., and Coffin, J.M. 2000.
The mouse mammary tumor virus transcription enhancers
for hematopoietic progenitor and mammary gland cells
share functional elements. J. Virol 74:
8183-8187.
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Tovar Sepulveda, V.A., Berdel, B.,
Coffin, J.M., and Reuss, F.U. 2000. Mouse mammary
tumor virus superantigen expression is reduced by glucocorticoid
treatment. Virology 275: 98-106.
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Rouzine, I., and Coffin, J.M. 1999.
Technical Comment: T Cell turnover in HIV infection.
Science 284: 555a.
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Rouzine, I., and Coffin. J.M. 1999.
Search for the Mechanism of Genetic Variation in the pro Gene
of HIV. J. Virol. 73: 8167-8178. PubMed
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Johnson, W.E., and Coffin,
J.M. 1999. Constructing primate phylogenies
from ancient retrovirus sequences. Proc. Natl. Acad.
Sci. USA. 96: 10254-10260. PubMed
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Aschoff, J.M., 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.
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Rouzine, I., and Coffin, J.M. 1999.
Linkage disequilibrium test implies a large effective
population number for HIV in vivo. Proc. Natl. Acad.
Sci. USA 96:10254-10260. PubMed
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Tomonaga, K., and Coffin,
J.M. 1999. Structures of endogenous murine
leukemia virus long terminal repeats in wild mice:
Implication for evolution of MLV’s. J. Virol.
73:
4327-4340. PubMed
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Tomonaga, K., and Coffin,
J.M. 1998. Structure and distribution of endogenous
nonecotropic viruses in wild mice. J. Virol. 72:
8289-8300.
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Reuss, F.U., and Coffin, J.M. 1998.
Mouse mammary tumor virus superantigen expression in
B cells is regulated by a central enhancer within the pol gene.
J. Virol. 72: 6073-6082. PubMed
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| Coffin, J.M., Hughes,
S.H., and Varmus, H.E. Intermezzo: The interactions of
retroviruses and their hosts pp335-342 in Retroviruses.
(Coffin, J.M., Hughes, S.H., and Varmus, H.E., eds) Cold
Spring Laboratory Press. Cold Spring Harbor, NY. [Retroviruses
at the National Center for Biotechnology Information]
[Cold Spring Harbor
Laboratory Press] |
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