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List of works by Siobain Duffy

98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray.

scientific article published on June 2010

A Transducing Bacteriophage Infecting Staphylococcus epidermidis Contributes to the Expansion of a Novel Siphovirus Genus and Implies the Genus Is Inappropriate for Phage Therapy

scientific article published in 2023

A divergent variant of Grapevine leafroll-associated virus 3 is present in California

scientific article

A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics

scientific article published on 04 July 2012

A multispecies polyadenylation site model ⬇️

scientific article published on January 21, 2013

Advances in plant virus evolution: translating evolutionary insights into better disease management

scientific article published in October 2011

An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing

scientific article published in 2022

Analysis and modeling of the variability associated with UV inactivation of Escherichia coli in apple cider.

scientific article published in November 2000

Antibiotic resistance correlates with transmission in plasmid evolution.

scientific article published on 24 November 2014

Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses ⬇️

scientific article published on January 15, 2013

Bioinformatic analysis reveals genome size reduction and the emergence of tyrosine phosphorylation site in the movement protein of New World bipartite begomoviruses

scientific article

Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses

scientific article published on 09 January 2014

Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts.

scientific article published on 15 July 2014

Dating the origins of the maize-adapted strain of maize streak virus, MSV-A.

scientific article

Diverse circovirus-like genome architectures revealed by environmental metagenomics

scientific article

Evolution of host specificity drives reproductive isolation among RNA viruses

scientific article published in October 2007

Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6

scientific article

Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

scientific article published on 16 July 2009

Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies

scientific article

Frequent coinfection reduces RNA virus population genetic diversity

scientific article published on 4 July 2013

Genetic diversity in the 3' terminal 4.7-kb region of grapevine leafroll-associated virus 3.

scientific article published on April 2011

Genus-specific substitution rate variability among picornaviruses

scientific article published on 25 May 2011

Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2

scientific article

Interspecies Recombination Has Driven the Macroevolution of Cassava Mosaic Begomoviruses

scientific article published on 13 June 2021

Modeling of combined processing steps for reducing Escherichia coli O157:H7 populations in apple cider.

scientific article

Modeling yeast spoilage in cold-filled ready-to-drink beverages with Saccharomyces cerevisiae, Zygosaccharomyces bailii, and Candida lipolytica.

scientific article published on April 2002

Modelling mould spoilage in cold-filled ready-to-drink beverages by Aspergillus niger and Penicillium spinulosum

Monte Carlo simulation of the risk of contamination of apples with Escherichia coli O157:H7.

scientific article

Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World ⬇️

scientific article

Occurrence of grapevine leafroll-associated virus complex in Napa Valley.

scientific article published on 19 October 2011

Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus

scientific article

Pleiotropic costs of niche expansion in the RNA bacteriophage phi 6.

scientific article

Point mutation rate of bacteriophage PhiX174.

scientific article published on 3 August 2009

Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation

scientific article published in 2021

Rates of evolutionary change in viruses: patterns and determinants

scientific article (publication date: April 2008)

Single-cell genomics reveals organismal interactions in uncultivated marine protists.

scientific article

Single-stranded genomic architecture constrains optimal codon usage ⬇️

scientific article published on July 1, 2011

Site-specific, enzymatic biotinylation of recombinant proteins in Spodoptera frugiperda cells using biotin acceptor peptides.

scientific article published on September 1998

Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts.

scientific article published on 7 November 2012

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

scientific article published on 22 January 2018

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

scientific article published on 11 March 2020

Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses

scientific article

Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and Old Worlds

scientific article

Why are RNA virus mutation rates so damn high?

scientific article published on 13 August 2018

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