Siobain Duffy

Summary

Affiliation: Rutgers University
Country: USA

Publications

  1. pmc Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses
    Allison L Hicks
    Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
    PLoS Pathog 10:e1003838. 2014
  2. pmc Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6
    Paul E Turner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:153. 2012
  3. pmc Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts
    Gordon W Harkins
    South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
    Virol J 6:104. 2009
  4. doi request reprint Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Gen Virol 90:1539-47. 2009
  5. pmc Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Virol 82:957-65. 2008
  6. pmc A divergent variant of Grapevine leafroll-associated virus 3 is present in California
    Yeemey Seah
    Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
    Virol J 9:235. 2012
  7. doi request reprint Rates of evolutionary change in viruses: patterns and determinants
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:267-76. 2008
  8. pmc One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate
    Allison L Hicks
    Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
    BMC Evol Biol 12:74. 2012
  9. pmc Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2
    Cadhla Firth
    Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 83:12813-21. 2009
  10. pmc A multispecies polyadenylation site model
    Eric S Ho
    Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
    BMC Bioinformatics 14:S9. 2013

Collaborators

Detail Information

Publications16

  1. pmc Cell Tropism Predicts Long-term Nucleotide Substitution Rates of Mammalian RNA Viruses
    Allison L Hicks
    Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
    PLoS Pathog 10:e1003838. 2014
    ..Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. ..
  2. pmc Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6
    Paul E Turner
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:153. 2012
    ..The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts)...
  3. pmc Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts
    Gordon W Harkins
    South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
    Virol J 6:104. 2009
    ..The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur...
  4. doi request reprint Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Gen Virol 90:1539-47. 2009
    ..We also validated our rate estimates by comparing them with those depicting the emergence of TYLCV in North America. These results further support the notion that geminiviruses evolve as rapidly as many RNA viruses...
  5. pmc Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Virol 82:957-65. 2008
    ..Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts...
  6. pmc A divergent variant of Grapevine leafroll-associated virus 3 is present in California
    Yeemey Seah
    Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
    Virol J 9:235. 2012
    ..During a survey of Napa Valley vineyards (California, USA), we found evidence of a new variant of Grapevine leafroll-associated virus 3 (GLRaV-3). We isolated its genome from a symptomatic greenhouse-raised plant and fully sequenced it...
  7. doi request reprint Rates of evolutionary change in viruses: patterns and determinants
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:267-76. 2008
    ....
  8. pmc One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate
    Allison L Hicks
    Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
    BMC Evol Biol 12:74. 2012
    ....
  9. pmc Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2
    Cadhla Firth
    Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 83:12813-21. 2009
    ..This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide...
  10. pmc A multispecies polyadenylation site model
    Eric S Ho
    Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
    BMC Bioinformatics 14:S9. 2013
    ..These methods typically use a large number of features, which increases the dimensionality of the models to crippling degrees, and typically are not validated against many kinds of genomes...
  11. pmc Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Appl Environ Microbiol 73:7114-7. 2007
    ..This analysis supports a second introduction of this Old World begomovirus into the New World, most likely from Asia...
  12. pmc Base composition and translational selection are insufficient to explain codon usage bias in plant viruses
    Daniel J Cardinale
    Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
    Viruses 5:162-81. 2013
    ..Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts...
  13. pmc 98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray
    Siobain Duffy
    Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
    Philos Trans R Soc Lond B Biol Sci 365:1891-7. 2010
    ..An increased use of phylogenetic methods in short-form publications could speed our understanding of these cryptic second introductions and aid in control of epidemics...
  14. pmc Genus-specific substitution rate variability among picornaviruses
    Allison L Hicks
    Department of Ecology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
    J Virol 85:7942-7. 2011
    ..Both a structural and a nonstructural gene show that enteroviruses are evolving, on average, a half order of magnitude faster than members of other genera within the Picornaviridae family...
  15. ncbi request reprint Frequent coinfection reduces RNA virus population genetic diversity
    John J Dennehy
    Department of Biology, Queens College, Flushing, NY 11367, USA
    J Hered 104:704-12. 2013
    ..Our results bolster a growing literature suggesting that RNA virus segmentation is probably not a mechanism that evolved because it provides a generalized benefit of sex...