J.S. Hoyer, O.W. Wilkins, A. Munshi, E. Weise, D. Dubey, S. Renard, K.R.H. Mortensen, A.E. Dye, I. Carbone, S. Duffy and J.T. Ascencio-Ibáñez. 2022. Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana. Phytobiomes Journal, in press.
A.A. Crespo-Bellido and S. Duffy. 2022. Strand-specific patterns of codon usage bias across Cressdnaviricota. Frontiers in Virology, 2:899608.
C.D. Aimone, J.S. Hoyer, A.E. Dye, D.O. Deppong, S. Duffy, I. Carbone and L. Hanley-Bowdoin. 2022. An experimental strategy for preparing circular ssDNA viruses for next-generation sequencing. Journal of Virological Methods, 300:114405.
L. Zhao, E. Lavington and S. Duffy. 2021. Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life. Journal of Evolutionary Biology, 34:1901-1916.
A. Crespo-Bellido, J.S. Hoyer, D. Dubey, R. Jeannot and S. Duffy. 2021. . Interspecies recombination has driven the macroevolution of cassava mosaic begomoviruses. Journal of Virology, 95:e00541-21.
C.D. Aimone, E. Lavington, J.S. Hoyer, D.O. Deppong, L. Mickelson-Young, A. Jacobson, G.G. Kennedy, I. Carbone, L. Hanley-Bowdoin and S. Duffy. 2021. Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation. Journal of General Virology, 102:001622.
R. Sanjuán, C. Illingworth, J. Geoghegan, J. Iranzo, M. Zwart, A. Ciota, G. Moratorio, S. Gago-Zachert, S. Duffy and D. Vijaykrishna. 2021. Five challenges in the field of viral diversity and evolution. Frontiers in Virology, 1:684949.
J.S. Hoyer, V.N. Fondong, M.M. Dallas, C. Doyle Aimone, D.O. Deppong, S. Duffy and L. Hanley-Bowdoin. 2020. Deeply sequenced infectious clones of key cassava begomovirus isolates from Cameroon. Microbial Resource Announcements, 9:e00802-20.
L. Williams, C. Cugini and S. Duffy. 2020. Two nearly complete nosocomial pathogen genomes reconstructed from early-middle 20th century dental calculus. Microbial Resource Announcements, 9:e00850-20.
E.M. Adriaenssens, M.B. Sullivan, P. Knezevic, L.J. van Zyl, B.L. Sarkar, B.E. Dutilh, P. Alfenas-Zerbini, M. Lobocka, Y. Tong, J.R. Brister, A.I. Moreno Swift, J. Klumpp, R. Karam Aziz, J. Barylski, J. Uchiyama, R.A. Edwards, A.M. Kropinski, N.K. Petty, M.R.C. Clokie, A.I. Kushkina, V.V. Morozova, S. Duffy, A. Gillis, J. Rumnieks, I. Kurtboke, N. Chanishvili, L. Goodridge, J. Wittmann, R. LAvigne, H.B. Jang, D. Prangishvili, F. Enault, D. Turner, M.M. Poranen, H. Oksanen and M. Krupovic. 2020. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology, 165:1253-1260.
L. Zhao and and S. Duffy. Gauging genetic diversity of generalists: a test of genetic and ecological
generalism with RNA virus experimental evolution. Virus Evolution, 5:vez019.
L. Zhao, M. Seth-Pasricha, D. Stemate, A. Crespo-Bellido, J. Gagnon and S. Duffy. 2019. Existing host range mutations constrain further emergence of RNA viruses. Journal of Virology, 93:e01385-18.
A.L. Jacobson, S. Duffy and P. Sseruwagi. 2018. Whitefly-transmitted viruses threatening cassava production in Africa. Current Opinion in Virology, 33:167-176.
S. Duffy. 2018. Why are RNA virus mutation rates so damn high? PLOS Biology, 16:e3000003.
E.M. Adriaenssens, J. Wittmann, J.H. Kuhn, D. Turner, M.B. Sullivan, B.E. Dutilh, H.B. Jang, L.J. van Zyl, J. Klumpp, M. Lobocka, A.I. Morena Switt, J. Rumnieks, R.A. Edwards, J. Uchiyama, P. Alfenas-Zerbini, N.K. Petty, A.M. Kropinski, J. Barylski, A. Gillia, M.R. Clokie, D. Prangishvili, R. Lavigne, R.K. Aziz, S. Duffy, M. Krupovic, M.M. Poranen, P. Knezevis, F. Enault. Y. Tong, H.M. Oksanen and J.R. Brister. 2018. Taxonomy of prokaryotic viruses: 2017 update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 163:1125-1129.
W. Mbewe, S. Duffy, S. Mukasa, I. Benesi, F. Tairo, P. Sseruwagi, J. Ndunguru, S. Sheat, M. Koerbler and S. Winter. 2017. Variability in the P1 gene redefines phylogenetic relationships among Cassava brown streak viruses. Virology Journal, 14:118.
A. Lima, J. Silva, F. Silva, G. Castillo-Urquiza, F. Silva, Y.M. Seah, E. Mizubuti, S. Duffy, F.M. Zerbini. 2017. The diversification of begomovirus populations is predominantly driven by mutational dynamics. Virus Evolution, 3:vex005.
C.A. Faillace, N.S. Lorusso, and S. Duffy. 2017. Overlooking the smallest matter: viruses impact species invasions. Ecology Letters, 20:524-538.
E.M. Adriaenssens, M. Krupovic, P. Knezevic, H.W. Ackermann, J. Barylski, J.R. Brister, M.R. Clokie, S. Duffy, B.E. Dutilh, R.A. Edwards, F. Enault. H.B. Jang, J. Klumpp, A.M. Kropinski, R. Lavigne, M.M. Poranen, D. Prangishvili, J. Rumnieks, M.B. Sullivan, J. Wittmann, H.M. Oksanen, A. Gillis, J.H. Kuhn. 2017. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 162:1153-1157.
M. Krupovic, B.E. Dutilh, E.M. Adriaenssens, J. Wittmann, F.K. Vogensen, M.B. Sullivan, J. Rumnieks, D. Prangishvili, R. Lavigne, A.M. Kropinski, J. Klumpp, A. Gillis, F. Enault, R.A. Edwards, S. Duffy, M.R.C. Clokie, J. Barylski, H.W. Ackerman, J.H Kuhn. 2016. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 161:1095-1099.
K. Rosario, Y.M. Seah, C. Marr, A. Varsani, S. Kaberger, D. Stainton, E. Moriones, J.E. Polston, S. Duffy and M. Breitbart. 2015. Vector-enabled metagenomic (VEM) surveys using whiteflies (Aleyrodidae) reveal novel begomovirus species in the New and Old Worlds. Viruses, 7: 5553-5570.
P.E. Turner, E.S.C.P. Williams, C. Okeke, V.S. Cooper, S. Duffy and J. Wertz. 2014. Antibiotic resistance correlates with transmission in plasmid evolution. Evolution. 12:3368-3380.
E.S. Ho, J. Kuchie and S. Duffy. 2014. Bioinformatic analysis reveals the emergence of tyrosine phosphorylation site in the movement protein of New World begomoviruses. PLoS One, 9:e111957.
M. Lapidot, D. Gelbart, A. Gal-On, N. Sela, G. Anfoka, F.H. Ahmed, Y. Abou-Jawada, H. Soboh, H. Mazaya, A.E, Aboul-Ata, A.K. El-Attar, M.S. Ali-Shtayeh, R.M. Jamous, J.E. Polston S. Duffy. 2014. Frequent migration of introduced cucurbit-infecting begomoviruses among Middle Eastern countries. Virology Journal, 11:181.
R.R. Sobrinho, C.A.D. Xavier, H.M.d.B. Pereira, G.S.A. de Lima, I.P. Assuncao, E.S.G. Mizubuti, S. Duffy and F.M. Zerbini. 2014. Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts. Journal of General Virology, 95:2540-2552.
A.L. Hicks and S. Duffy. 2014. Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. PLoS Pathogens, 10:e1003838.
J. Dennehy, S. Duffy, K.J. O’Keefe, S.V. Edwards and P.E. Turner. 2013. Frequent coinfection reduces RNA virus population genetic diversity. Journal of Heredity, 104:704-712.
E.S. Ho, S.I. Gunderson and S. Duffy. 2013. A multispecies polyadenylation site model. BMC Bioinformatics, 14:S9.
D.J. Cardinale, K. DeRosa and S. Duffy. 2013. Base composition and translational selection are insufficient to explain codon usage bias in plant viruses. Viruses, 5:162-181.
A.T.M. Lima, R.R. Sobrinho, J. Gonzalez-Aguilera, C.S. Rocha, S.J.C. Silca, C.A.D. Xavier, F.N. Silva, S. Duffy and F.M. Zerbini. 2013. Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts. Journal of General Virology, 94:418-431.
Y.M. Seah, A. Sharma, S, Zhang, R.P.P. Almeida and S. Duffy. 2012. A divergent variant of Grapevine leafroll-associated virus 3 is present in California. Virology Journal, 9:235.
K. Rosario, S. Duffy and M. Breitbart. 2012. A field guide to eukaryotic circular single-stranded DNA viruses: Insights gained from metagenomics. Archives of Virology, 157:1851-1871.
P.E. Turner, R.C. McBride, S. Duffy, R. Montville, L.S. Wang, Y. Yang, S.J. Lee and J. Kim. 2012. Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6. BMC Evolutionary Biology. 12:153.
A.L. Hicks and S. Duffy. 2012. One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate. BMC Evolutionary Biology. 12:74.
D.J. Cardinale and S. Duffy. 2011. Bacteriophage genomic architecture constrains optimal codon usage. Bacteriophage. 1:219-224.
A. Sharma, J. Wang, S. Duffy, S, Zhang, M. Wong, A. Rashed, M. Cooper, K. Daane, and R. Almeida. 2011. Hierarchical genetic analysis of a plant disease caused by a virus complex. PLoS One. 6:e26227.
R. Acosta-Leal, S. Duffy, Z. Xiong, R. Hammond, and S.F. Elena. 2011. Advances in plant virus evolution: Translating evolutionary insights into better disease management. Phytopathology. 101:1136-1148.
A.L. Hicks and S. Duffy. 2011. Genus-specific substitution rate variability among picornaviruses. Journal of Virology. 85:7942-7947.
H.S. Yoon, D.C. Price, R. Stepanauskas, V.D. Rajah, M.E. Sieracki, W.H. Wilson, E.C. Yang, S. Duffy, and D. Bhattacharya. 2011. Single cell genomics reveals trophic interactions and evolutionary history of uncultured protists. Science. 332:714-717.
T.F.F. Ng, S. Duffy, E. Bixby, G.E Vallad, J.E. Polston, and M. Breitbart. 2011. Exploring the diversity of plant viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One. 6:e19050.
J. Wang, A.M. Sharma, S. Duffy, and R.P.P. Almeida. 2011. Genetic diversity at the 3’ terminal region of Grapevine leafroll-associated virus 3. Phytopathology. 101:445-450.
S. Duffy and Y.M. Seah. 2010. 98% identical, 100% wrong: percent nucleotide identity can lead plant virus epidemiology astray. Philosophical Transactions of the Royal Society B. 365:1891-1897.
C. Firth, M.A. Charleston, S. Duffy, B. Shapiro and E.C. Holmes. 2009. Insights into the evolutionary history of an emerging livestock pathogen: Porcine circovirus 2. Journal of Virology. 83:12813-12821.
G.W. Harkins, D.P. Martin, S. Duffy, A,L. Monjane, D.N. Shepherd, O.P. Windram, B.E. Owor, L. Donaldson, T. van Antwerpen, R.A. Sayed, B. Flett, M. Ramusi, E.P. Rybicki, M. Peterschmitt and A. Varsani. 2009. Dating the origins of the maize-adapted strain of maize streak virus MSV-A. Journal of General Virology. 90:3066-3074.
J.M. Cuevas, S. Duffy and R. Sanjuán. 2009. Point mutation rate of phiX174. Genetics. 183:747-749.
K. Rosario, S. Duffy and M. Breitbart. 2009. Diverse circovirus-like genome architectures revealed by environmental metagenomics. Journal of General Virology. 90:2418-2424.
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 and E.C. Holmes. 2009. Validation of high rates of nucleotide substitution in geminiviruses: Phylogenetic evidence from East African cassava mosaic viruses. Journal of General Virology. 90:1539-1547.
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.
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.
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.
BOOK CHAPTERS
L. Bono and S. Duffy. 2020. Mechanisms of RNA virus evolution. Chapter 5, p.62-70 in Encyclopedia of Virology. Elsevier.
W. Mbewe, L. Hanley-Bowdoin, J. Ndunguru and S. Duffy. 2020. Cassava viruses – host jumps, virus recombination, spread in plant material. Chapter 7, p.133-157 in Emerging Plant Diseases and Global Food Security. A. Records, J. Ristaino, eds. APS Press.
L. Zhao, K. Rosario, M. Breitbart and S. Duffy. Eukaryotic Circular Rep-encoding Single-Stranded DNA (CRESS DNA) viruses: ubiquitous viruses with small genomes and a diverse host range. Chapter 3 in Advances in Virus Research, 103: 71-133. M. Kielian, T.C. Mettenleiter, M.J. Roossinck. Elsevier.
S. Duffy. Viral informatics: tools for understanding the evolution of biology’s most varied genomes. 2016. In Viral Evolution. S.C. Weaver, M.R. Denison, M. Roossinck, M. Vignuzzi, eds. Horizon Press.
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.
Publications