Select Publications
Journal articles
2024, 'Low HIV drug resistance prevalence among recently diagnosed HIV-positive men who have sex with men in a setting of high PrEP use', Journal of the International AIDS Society, 27, http://dx.doi.org/10.1002/jia2.26308
,2024, 'Molecular epidemiology of the HIV-1 epidemic in Fiji', npj Viruses, 2, http://dx.doi.org/10.1038/s44298-024-00019-3
,2024, 'Molecular epidemiology to aid virtual elimination of HIV transmission in Australia', Virus Research, 341, http://dx.doi.org/10.1016/j.virusres.2024.199310
,2023, 'Novel siRNA therapeutics demonstrate multi-variant efficacy against SARS-CoV-2', Antiviral Research, 217, http://dx.doi.org/10.1016/j.antiviral.2023.105677
,2023, 'Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021', Viruses, 15, http://dx.doi.org/10.3390/v15010016
,2022, 'Reemergence of an atypical bluetongue virus strain in goats, Sardinia, Italy', Research in Veterinary Science, 151, pp. 36 - 41, http://dx.doi.org/10.1016/j.rvsc.2022.07.003
,2022, 'First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa', Acta Tropica, 232, http://dx.doi.org/10.1016/j.actatropica.2022.106482
,2022, 'Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia', Pathogens, 11, http://dx.doi.org/10.3390/pathogens11070758
,2022, 'Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern', Epidemics, 39, http://dx.doi.org/10.1016/j.epidem.2022.100578
,2021, 'Infectious disease phylodynamics with occurrence data', Methods in Ecology and Evolution, 12, pp. 1498 - 1507, http://dx.doi.org/10.1111/2041-210X.13620
,2021, 'HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection', JCI Insight, 6, http://dx.doi.org/10.1172/jci.insight.143940
,2021, 'Emergence and spread of sars-cov-2 lineages b.1.1.7 and p.1 in Italy', Viruses, 13, http://dx.doi.org/10.3390/v13050794
,2021, 'Erratum: Virome composition in marine fish revealed by meta-transcriptomics (Virus Evolution (2021) 7:1 (veab005) DOI: 10.1093/ve/veab005)', Virus Evolution, 7, http://dx.doi.org/10.1093/ve/veab035
,2021, 'Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR', Emerging Microbes and Infections, 10, pp. 1148 - 1155, http://dx.doi.org/10.1080/22221751.2021.1933609
,2021, 'Subtype-specific differences in transmission cluster dynamics of HIV-1 B and CRF01_AE in New South Wales, Australia', Journal of the International AIDS Society, 24, pp. e25655, http://dx.doi.org/10.1002/jia2.25655
,2021, 'Virome composition in marine fish revealed by meta-transcriptomics', Virus Evolution, 7, http://dx.doi.org/10.1093/ve/veab005
,2020, 'Conserved epitopes with high HLA-I population coverage are targets of CD8+ T cells associated with high IFN-γ responses against all dengue virus serotypes', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-77565-2
,2020, 'Genomic epidemiology of the first wave of sars-cov-2 in Italy', Viruses, 12, http://dx.doi.org/10.3390/v12121438
,2020, 'Increased hiv subtype diversity reflecting demographic changes in the hiv epidemic in new south wales, australia', Viruses, 12, pp. 1402, http://dx.doi.org/10.3390/v12121402
,2020, 'Red fox viromes in urban and rural landscapes', Virus Evolution, 6, http://dx.doi.org/10.1093/ve/veaa065
,2019, 'Limited sustained local transmission of HIV-1 CRF01_AE in New South Wales, Australia', Viruses, 11, pp. 482, http://dx.doi.org/10.3390/v11050482
,2019, 'Punctuated evolution of myxoma virus: Rapid and disjunct evolution of a recent viral lineage in Australia', Journal of Virology, 93, http://dx.doi.org/10.1128/JVI.01994-18
,2019, 'Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture', Virus Evolution, 5, http://dx.doi.org/10.1093/ve/vez012
,2018, 'Hidden diversity and evolution of viruses in market fish', Virus Evolution, 4, pp. vey031 - vey031, http://dx.doi.org/10.1093/ve/vey031
,2018, 'Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia', Viruses, 10, http://dx.doi.org/10.3390/v10090476
,2018, 'HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia', Future Virology, 13, pp. 575 - 584, http://dx.doi.org/10.2217/fvl-2018-0031
,2018, 'Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line', Journal of General Virology, 99, pp. 832 - 836, http://dx.doi.org/10.1099/jgv.0.001079
,2018, 'A10 Using the molecular epidemiology of HIV transmission in New South Wales to inform public health response: Assessing the representativeness of linked phylogenetic data', Virus Evolution, 4, http://dx.doi.org/10.1093/ve/vey010.009
,2017, 'Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species', Journal of Virology, 91, http://dx.doi.org/10.1128/JVI.02381-16
,2017, 'RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation', PLoS Pathogens, 13, http://dx.doi.org/10.1371/journal.ppat.1006155
,2016, 'Cross-validation to select Bayesian hierarchical models in phylogenetics', BMC Evolutionary Biology, 16, http://dx.doi.org/10.1186/s12862-016-0688-y
,2016, 'Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4 + T cells', Scientific Reports, 6, http://dx.doi.org/10.1038/srep24157
,2016, 'Virological factors that increase the transmissibility of emerging human viruses', Proceedings of the National Academy of Sciences of the United States of America, 113, pp. 4170 - 4175, http://dx.doi.org/10.1073/pnas.1521582113
,2016, 'Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants', Clinical Microbiology and Infection, 22, pp. 191 - 200, http://dx.doi.org/10.1016/j.cmi.2015.10.004
,2016, 'A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations', Journal of Molecular Biology, 428, pp. 238 - 250, http://dx.doi.org/10.1016/j.jmb.2015.12.012
,2016, 'A follow-up of the multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 ultra deep pyrosequencing', PLoS ONE, 11, http://dx.doi.org/10.1371/journal.pone.0146687
,2016, 'Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of hepadnaviruses', Journal of Virology, 90, pp. 7920 - 7933, http://dx.doi.org/10.1128/JVI.00832-16
,2016, 'Fluid spatial dynamics of West Nile virus in the United States: Rapid spread in a permissive host environment', Journal of Virology, 90, pp. 862 - 872, http://dx.doi.org/10.1128/JVI.02305-15
,2016, 'Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales', Molecular Biology and Evolution, 33, pp. 255 - 267, http://dx.doi.org/10.1093/molbev/msv207
,2015, 'Exploring Host–Pathogen Interactions through Biological Control', PLoS Pathogens, 11, http://dx.doi.org/10.1371/journal.ppat.1004865
,2015, 'A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory (vol 199, pg 191, 2014)', GENETICS, 199, pp. 1271 - 1271, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000352734400028&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
,2015, 'Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: A multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing', Journal of Antimicrobial Chemotherapy, 70, pp. 930 - 940, http://dx.doi.org/10.1093/jac/dku426
,2015, 'Viral biocontrol: Grand experiments in disease emergence and evolution', Trends in Microbiology, 23, pp. 83 - 90, http://dx.doi.org/10.1016/j.tim.2014.10.004
,2015, 'A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory', Genetics, 199, pp. 191 - 203, http://dx.doi.org/10.1534/genetics.114.172312
,2014, 'Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations', Nucleic Acids Research, 42, http://dx.doi.org/10.1093/nar/gku537
,2014, 'An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing', Journal of Virological Methods, 204, pp. 31 - 37, http://dx.doi.org/10.1016/j.jviromet.2014.04.007
,2013, 'Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination', PLoS ONE, 8, http://dx.doi.org/10.1371/journal.pone.0074249
,2012, 'EH3 (ABHD9): The first member of a new epoxide hydrolase family with high activity for fatty acid epoxides', Journal of Lipid Research, 53, pp. 2038 - 2045, http://dx.doi.org/10.1194/jlr.M024448
,2012, 'Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells', Retrovirology, 9, http://dx.doi.org/10.1186/1742-4690-9-27
,2011, 'Reappearance of minority K103N HIV-1 variants after interruption of ART initiated during primary HIV-1 infection', PLoS ONE, 6, http://dx.doi.org/10.1371/journal.pone.0021734
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