John Coffin

Summary

Affiliation: Tufts University
Country: USA

Publications

  1. pmc Virions at the gates: receptors and the host-virus arms race
    John M Coffin
    Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
    PLoS Biol 11:e1001574. 2013
  2. pmc HIV pathogenesis: dynamics and genetics of viral populations and infected cells
    John Coffin
    Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
    Cold Spring Harb Perspect Med 3:a012526. 2013
  3. pmc Binding of more than one Tva800 molecule is required for ASLV-A entry
    Eleanor R Gray
    Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
    Retrovirology 8:96. 2011
  4. pmc Mouse DNA contamination in human tissue tested for XMRV
    Mark J Robinson
    Section of Infectious Diseases, Jefferiss Research Trust Laboratories, Imperial College London, St Mary s Campus, London, W2 1PG, UK
    Retrovirology 7:108. 2010
  5. pmc Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences
    Brendan Oakes
    Department of Pathology, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA
    Retrovirology 7:109. 2010
  6. pmc Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses
    Ravi P Subramanian
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
    Retrovirology 8:90. 2011
  7. pmc Characterization, mapping, and distribution of the two XMRV parental proviruses
    Oya Cingoz
    Department of Molecular Biology and Microbiology, Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
    J Virol 86:328-38. 2012
  8. pmc Multi-site adaptation in the presence of infrequent recombination
    Igor M Rouzine
    Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA 02111, USA
    Theor Popul Biol 77:189-204. 2010
  9. doi request reprint Effects of retroviruses on host genome function
    Patric Jern
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
    Annu Rev Genet 42:709-32. 2008
  10. pmc The solitary wave of asexual evolution
    Igor M Rouzine
    Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
    Proc Natl Acad Sci U S A 100:587-92. 2003

Research Grants

  1. RETROVIRUS EVOLUTION
    John Coffin; Fiscal Year: 2007
  2. Integration and Expression of Retrovirus DNA
    John Coffin; Fiscal Year: 2005
  3. RETROVIRUS EVOLUTION
    John Coffin; Fiscal Year: 2005

Collaborators

  • I M Rouzine
  • Patric Jern
  • J Wakeley
  • Oya Cingoz
  • Ravi P Subramanian
  • Eleanor R Gray
  • Mark J Robinson
  • Brendan Oakes
  • G Jonah A Rainey
  • Krista A Delviks-Frankenberry
  • Vinay K Pathak
  • Sheryl Wildt
  • Tobias Paprotka
  • WEI SHAU HU
  • Crystal Russo
  • Julia H Wildschutte
  • Jonathan P Stoye
  • Christopher J R Illingworth
  • Jonathan Weber
  • Susan Levine
  • Marjorie M Walker
  • Anup Patel
  • Mongkol Uiprasertkul
  • Otto W Erlwein
  • Madeleine H Henefield
  • Wun Jae Kim
  • Myra O McClure
  • Brigitte T Huber
  • Albert K Tai
  • Steve Kaye

Detail Information

Publications11

  1. pmc Virions at the gates: receptors and the host-virus arms race
    John M Coffin
    Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
    PLoS Biol 11:e1001574. 2013
    ..could find no evidence of TfR1 mutations in this region that might have been selected as a consequence of human infection, the authors identified one such mutation in Asian populations that affects infection with these viruses...
  2. pmc HIV pathogenesis: dynamics and genetics of viral populations and infected cells
    John Coffin
    Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
    Cold Spring Harb Perspect Med 3:a012526. 2013
    ..These studies have revealed important features of the virus-host interaction that now form the basis of our understanding of the importance and consequence of ongoing viral replication during HIV-1 infection...
  3. pmc Binding of more than one Tva800 molecule is required for ASLV-A entry
    Eleanor R Gray
    Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
    Retrovirology 8:96. 2011
    ..In these studies, we have now investigated the number of target receptors necessary for entry of ASLV Env-pseudotyped virions...
  4. pmc Mouse DNA contamination in human tissue tested for XMRV
    Mark J Robinson
    Section of Infectious Diseases, Jefferiss Research Trust Laboratories, Imperial College London, St Mary s Campus, London, W2 1PG, UK
    Retrovirology 7:108. 2010
    ..To control for contamination, PCR assays to detect either mouse mitochondrial DNA (mtDNA) or intracisternal A particle (IAP) long terminal repeat DNA were run on all samples, owing to their very high copy number in mouse cells...
  5. pmc Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences
    Brendan Oakes
    Department of Pathology, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA
    Retrovirology 7:109. 2010
    ..Since there is a high degree of similarity between XMRV and abundant endogenous MLV proviruses, it is important to distinguish contaminating mouse sequences from true infections...
  6. pmc Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses
    Ravi P Subramanian
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
    Retrovirology 8:90. 2011
    ..Interestingly, this expression is upregulated in many tumors ranging from breast and ovarian tissues to lymphomas and melanomas, as well as schizophrenia, rheumatoid arthritis, and other disorders...
  7. pmc Characterization, mapping, and distribution of the two XMRV parental proviruses
    Oya Cingoz
    Department of Molecular Biology and Microbiology, Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
    J Virol 86:328-38. 2012
    ....
  8. pmc Multi-site adaptation in the presence of infrequent recombination
    Igor M Rouzine
    Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA 02111, USA
    Theor Popul Biol 77:189-204. 2010
    ..Interestingly, the strong effect of linkage on the adaptation rate is predicted in the absence of average linkage disequilibrium (Lewontin's measure)...
  9. doi request reprint Effects of retroviruses on host genome function
    Patric Jern
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
    Annu Rev Genet 42:709-32. 2008
    ....
  10. pmc The solitary wave of asexual evolution
    Igor M Rouzine
    Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
    Proc Natl Acad Sci U S A 100:587-92. 2003
    ..The model explains a logarithmic dependence of steady-state fitness on the population size reported recently for an RNA virus...
  11. pmc Evolution of broad host range in retroviruses leads to cell death mediated by highly cytopathic variants
    G Jonah A Rainey
    Department of Biochemistry, Tufts University School of Medicine, Boston, MA, USA
    J Virol 80:562-70. 2006
    ..Previously, we have shown that the mutants exhibit diminished resistance to superinfection. The results presented here have important implications for the process of evolution of retroviruses to use distinct cellular receptors...

Research Grants13

  1. RETROVIRUS EVOLUTION
    John Coffin; Fiscal Year: 2007
    ..Understanding of both how this evolution has occurred in our past and how it occurs in simple models will leave us better prepared to deal with such events as they happen. ..
  2. Integration and Expression of Retrovirus DNA
    John Coffin; Fiscal Year: 2005
    ..role of the integration site in the level of transcription of the integrated provirus? In particular, what is the basis for "position effects" leading to clone-to-clone variation in expression of integrated proviruses? ..
  3. RETROVIRUS EVOLUTION
    John Coffin; Fiscal Year: 2005
    ....