J.M. Cuevas, S. Duffy and R. Sanjuán. 2009. Mutation rate of phiX174. Genetics. In press. K. Rosario, S. Duffy and M. Breitbart. 2009. Diverse circovirus-like genome architectures revealed by environmental metagenomics. Journal of General Virology. In press G. Harkins, W. Delport, S. Duffy, N. Wood, A,L. Monjane, B.E. Owor, L. Donaldson, S. Saumtally, S. Verabudren, G. Triton, P.G. Markham, R.W. Briddon, D.N. Shepherd, E.P. Rybicki, D.P. Martin and A. Varsani. 2009. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virology Journal. 6:104. S. Duffy, L. A. Shackelton and E.C. Holmes. 2008. Rates of evolutionary change in viruses: patterns and determinants. Nature Reviews Genetics. 9:267-276. S. Duffy and E.C. Holmes. 2008. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus (TYLCV). Journal of Virology. 82:957-965. S. Duffy and E.C. Holmes. 2007. Multiple introductions of Tomato yellow leaf curl virus into the new world. Applied and Environmental Microbiology. 73:7114-7117. S. Duffy, C.L. Burch and P.E. Turner. 2007. Evolution of host specificity drives reproductive isolation among RNA viruses. Evolution. 61:2614-2622. Highlighted in The Economist: A god of small things, 10/6/07, p.96. Faculty of 1000, “must read,” 5/16/08 S. Duffy, P.E. Turner and C.L. Burch. 2006. Pleiotropic costs of niche expansion in the RNA bacteriophage phi6. Genetics. 172:1-7. PREDICTIVE FOOD MICROBIOLOGY D.W. Schaffner, J. McEntire, S. Duffy, R. Montville, and S. Smith. 2003. Monte Carlo simulation of the shelf life of pasteurized milk as affected by temperature and initial concentration of spoilage organisms. Food Protection Trends. 23:1014-1021. S. Duffy and D.W. Schaffner. 2002. Modeling the environmental contamination of apples with Escherichia coli O157:H7. International Journal of Food Microbiology. 78:245-255. T.M. Ng, E. Viard, M.L. Caipo, S. Duffy and D.W. Schaffner. 2002. Expansion and validation of a predictive model for the growth of Bacillus stearothermophilus in military rations. Journal of Food Science. 67:1872-1878. M.L. Caipo, S. Duffy, L. Zhao and D.W. Schaffner. 2002. Inoculum size affects germination of Bacillus megaterium. Journal of Applied Microbiology, 92:879-884. A.S. Battey, S. Duffy and D.W. Schaffner. 2002. Modeling yeast spoilage in cold-filled ready-to-drink beverages. Applied and Environmental Microbiology. 68:1901-1906. A.S. Battey, S. Duffy and D.W. Schaffner. 2001. Modelling mould spoilage in cold-filled ready-to-drink beverages by Aspergillus niger and Penicillium spinulosum. Food Microbiology. 18:521-529. M.K. Llaudes, L. Zhao, S. Duffy and D.W. Schaffner. 2001. Simulation and modelling of the effect of small inoculum size on time to spoilage by Bacillus stearothermophilus. Food Microbiology. 18:395-405. S. Duffy and D.W. Schaffner. 2001. Modeling the survival of Escherichia coli O157:H7 in apple cider using probability distribution functions for quantitative risk assessment. Journal of Food Protection. 64:599–605. H.E. Uljas, D.W. Schaffner, S. Duffy and S.C. Ingham. 2001. Modeling of combined processing steps for reducing Escherichia coli O157:H7 populations in apple cider. Applied and Environmental Microbiology. 67:133-141. S. Duffy, D.W. Schaffner, J. Churey and R.W. Worobo 2000. Analysis and modeling of the variability associated with UV inactivation of Escherichia coli in apple cider. Journal of Food Protection. 63:1587–1590. MOLECULAR VIROLOGY S. Duffy, K.-L. Tsao and D.S. Waugh. 1998. Site-specific, enzymatic biotinylation of recombinant proteins in Spodoptera frugiperda cells using biotin acceptor peptides. Analytical Biochemistry. 262:122-128. BOOK CHAPTERS S.T. Abedon, S. Duffy and P.E. Turner. 2009. Bacteriophage, Ecology. p42-57 in Encyclopedia of Microbiology. 3rd edition, M. Schaechter, ed. Elsevier. S. Duffy and P.E. Turner. 2008. Phage evolutionary biology. Chapter 6, p.147-176, in Bacteriophage Ecology: Population Growth, Evolution and Impact of Bacterial Viruses. S.T. Abedon, ed. Cambridge University Press. P.E. Turner and S. Duffy. 2008. Evolutionary ecology of multiple phage adsorption and infection. Chapter 8, p.195-216, in Bacteriophage Ecology: Population Growth, Evolution and Impact of Bacterial Viruses. S.T. Abedon, ed. Cambridge University Press. S. Duffy, Y. Chen and D.W. Schaffner. 2002. Quantitative risk assessment of the safety of minimally processed foods. Chapter 8, p.165 -182, in The Microbial Safety of Minimally Processed Foods. J.S. Novak, G.M. Sapers and V.K. Juneja, eds. CRC Press.http://origin.www.nature.com/nrg/journal/v9/n4/abs/nrg2323.htmlhttp://jvi.asm.org/cgi/content/abstract/82/2/957http://aem.asm.org/cgi/content/abstract/73/21/7114http://www.blackwell-synergy.com/doi/abs/10.1111/j.1558-5646.2007.00226.x?journalCode=evohttp://www.economist.com/science/displaystory.cfm?story_id=9898305http://www.genetics.org/cgi/content/full/172/2/751http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T7K-45MWMTN-1&_user=10&_coverDate=10%2F25%2F2002&_rdoc=6&_fmt=summary&_orig=browse&_srch=doc-info(%23toc%235061%232002%23999219996%23330637%23FLA%23display%23Volume)&_cdi=5061&_sort=d&_docanchor=&_ct=11&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=2a5198fe7f2c98c0bb6fcd5788731aa1http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2621.2002.tb08739.xhttp://www.blackwell-synergy.com/doi/full/10.1046/j.1365-2672.2002.01597.xhttp://aem.asm.org/cgi/content/full/68/4/1901http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WFP-458NKKJ-N&_user=10&_coverDate=10%2F31%2F2001&_rdoc=6&_fmt=summary&_orig=browse&_srch=doc-info(%23toc%236800%232001%23999819994%23287644%23FLP%23display%23Volume)&_cdi=6800&_sort=d&_docanchor=&_ct=11&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=099bef3ef333c9e819e6a74a2306b189http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WFP-458NKM5-11&_user=10&_coverDate=08%2F31%2F2001&_rdoc=5&_fmt=summary&_orig=browse&_srch=doc-info(%23toc%236800%232001%23999819995%23287646%23FLP%23display%23Volume)&_cdi=6800&_sort=d&_docanchor=&_ct=12&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=1197867cbdd1c9426c2f640b30c62054http://apt.allenpress.com/perlserv/?request=get-abstract&doi=10.1043%2F0362-028X%282001%29064%5B0599%3AMTSOCO%5D2.3.CO%3B2http://aem.asm.org/cgi/content/full/67/1/133http://apt.allenpress.com/perlserv/?request=get-abstract&doi=10.1043%2F0362-028X%282000%29063%5B1587%3AAAMOTV%5D2.3.CO%3B2http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6W9V-45KKSW5-51&_user=10&_coverDate=09%2F10%2F1998&_alid=638619523&_rdoc=3&_fmt=summary&_orig=search&_cdi=6692&_sort=d&_docanchor=&view=c&_ct=31&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=485734a925c068f45501653211f8c8c9http://www.amazon.com/Bacteriophage-Ecology-Population-Evolution-Microbiology/dp/0521858453/ref=sr_1_1/002-5154020-3511229?ie=UTF8&s=books&qid=1193533036&sr=1-1http://www.amazon.com/Bacteriophage-Ecology-Population-Evolution-Microbiology/dp/0521858453/ref=sr_1_1/002-5154020-3511229?ie=UTF8&s=books&qid=1193533036&sr=1-1http://www.amazon.com/Microbial-Safety-Minimally-Processed-Foods/dp/1587160412/ref=sr_1_1/002-5154020-3511229?ie=UTF8&s=books&qid=1193532985&sr=8-1shapeimage_1_link_0shapeimage_1_link_1shapeimage_1_link_2shapeimage_1_link_3shapeimage_1_link_4shapeimage_1_link_5shapeimage_1_link_6shapeimage_1_link_7shapeimage_1_link_8shapeimage_1_link_9shapeimage_1_link_10shapeimage_1_link_11shapeimage_1_link_12shapeimage_1_link_13shapeimage_1_link_14shapeimage_1_link_15shapeimage_1_link_16shapeimage_1_link_17shapeimage_1_link_18
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