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Journal articles

Spedicato M; Compagni ED; Caporale M; Teodori L; Leone A; Ancora M; Mangone I; Perletta F; Portanti O; Di Giallonardo F; Bonfini B; Savini G; Lorusso A, 2022, 'Reemergence of an atypical bluetongue virus strain in goats, Sardinia, Italy', Research in Veterinary Science, vol. 151, pp. 36 - 41, http://dx.doi.org/10.1016/j.rvsc.2022.07.003

Molini U; Curini V; Jacobs E; Tongo E; Berjaoui S; Hemberger MY; Puglia I; Jago M; Khaiseb S; Cattoli G; Dundon WG; Lorusso A; Di Giallonardo F, 2022, 'First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa', Acta Tropica, vol. 232, http://dx.doi.org/10.1016/j.actatropica.2022.106482

Curini V; Marcacci M; Abid S; Ouederni M; Elmoussi A; Charaa L; Achour W; Ouhichi R; Maazaoui L; Di Pasquale A; Elghord H; Gzara A; Ripani A; Di Giallonardo F; Cammà C; Lorusso A; Boubaker IBB, 2022, 'Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia', Pathogens, vol. 11, pp. 758 - 758, http://dx.doi.org/10.3390/pathogens11070758

Amato L; Candeloro L; Di Girolamo A; Savini L; Puglia I; Marcacci M; Caporale M; Mangone I; Cammà C; Conte A; Torzi G; Mancinelli A; Di Giallonardo F; Lorusso A; Migliorati G; Schael T; D'Alterio N; Calistri P, 2022, 'Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern', Epidemics, vol. 39, pp. 100578, http://dx.doi.org/10.1016/j.epidem.2022.100578

Featherstone LA; Di Giallonardo F; Holmes EC; Vaughan TG; Duchêne S, 2021, 'Infectious disease phylodynamics with occurrence data', Methods in Ecology and Evolution, vol. 12, pp. 1498 - 1507, http://dx.doi.org/10.1111/2041-210X.13620

Geoghegan JL; Di Giallonardo F; Wille M; Ortiz-Baez AS; Costa VA; Ghaly T; Mifsud JCO; Turnbull OMH; Bellwood DR; Williamson JE; Holmes EC, 2021, 'Virome composition in marine fish revealed by meta-transcriptomics (vol 7, veab005, 2021)', VIRUS EVOLUTION, vol. 7, http://dx.doi.org/10.1093/ve/veab035

Kok YL; Vongrad V; Chaudron SE; Shilaih M; Leemann C; Neumann K; Kusejko K; Di Giallonardo F; Kuster H; Braun DL; Kouyos RD; Günthard HF; Metzner KJ, 2021, 'HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection', JCI Insight, vol. 6, http://dx.doi.org/10.1172/jci.insight.143940

Di Giallonardo F; Puglia I; Curini V; Cammà C; Mangone I; Calistri P; Cobbin JCA; Holmes EC; Lorusso A, 2021, 'Emergence and spread of sars-cov-2 lineages b.1.1.7 and p.1 in Italy', Viruses, vol. 13, pp. 794 - 794, http://dx.doi.org/10.3390/v13050794

Amato L; Jurisic L; Puglia I; Di Lollo V; Curini V; Torzi G; Di Girolamo A; Mangone I; Mancinelli A; Decaro N; Calistri P; Di Giallonardo F; Lorusso A; D’Alterio N, 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, vol. 10, pp. 1148 - 1155, http://dx.doi.org/10.1080/22221751.2021.1933609

Di Giallonardo F; Pinto AN; Keen P; Shaik A; Carrera A; Salem H; Selvey C; Nigro SJ; Fraser N; Price K; Holden J; Lee FJ; Dwyer DE; Bavinton BR; Geoghegan JL; Grulich AE; Kelleher AD; Guy R; Prestage G; Zablotska I; Duck T; Cooper C; Holt M; de Wit J; Kaldor J; Wilson D; Brotherton A; Cooper DA; Crooks L; Whittaker B; Callander D; Madeddu D; Schmidt HM; Telfer B; Boyd M; McGill S; Patel P; Power C; Gordon T; Feeney L; Bath K; Mackie B, 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, vol. 24, pp. e25655, http://dx.doi.org/10.1002/jia2.25655

Geoghegan JL; Di Giallonardo F; Wille M; Ortiz-Baez AS; Costa VA; Ghaly T; Mifsud JCO; Turnbull OMH; Bellwood DR; Williamson JE; Holmes EC, 2021, 'Virome composition in marine fish revealed by meta-transcriptomics', Virus Evolution, vol. 7, http://dx.doi.org/10.1093/ve/veab005

Adikari TN; Di Giallonardo F; Leung P; Grifoni A; Sette A; Weiskopf D; Bull RA; Luciani F, 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, vol. 10, http://dx.doi.org/10.1038/s41598-020-77565-2

Di Giallonardo F; Duchene S; Puglia I; Curini V; Profeta F; Cammà C; Marcacci M; Calistri P; Holmes EC; Lorusso A, 2020, 'Genomic epidemiology of the first wave of sars-cov-2 in Italy', Viruses, vol. 12, http://dx.doi.org/10.3390/v12121438

Di Giallonardo F; Pinto AN; Keen P; Shaik A; Carrera A; Salem H; Selvey C; Nigro SJ; Fraser N; Price K; Holden J; Lee FJ; Dwyer DE; Bavinton BR; Grulich AE; Kelleher AD, 2020, 'Increased hiv subtype diversity reflecting demographic changes in the hiv epidemic in new south wales, australia', Viruses, vol. 12, http://dx.doi.org/10.3390/v12121402

Campbell SJ; Ashley W; Gil-Fernandez M; Newsome TM; Di Giallonardo F; Ortiz-Baez AS; Mahar JE; Towerton AL; Gillings M; Holmes EC; Carthey AJR; Geoghegan JL, 2020, 'Red fox viromes in urban and rural landscapes', Virus Evolution, vol. 6, http://dx.doi.org/10.1093/ve/veaa065

Di Giallonardo F; Pinto AN; Keen P; Shaik A; Carrera A; Salem H; Telfer B; Cooper C; Price K; Selvey C; Holden J; Bachmann N; Lee FJ; Dwyer DE; Duchêne S; Holmes EC; Grulich AE; Kelleher AD, 2019, 'Limited sustained local transmission of HIV-1 CRF01_AE in New South Wales, Australia', Viruses, vol. 11, http://dx.doi.org/10.3390/v11050482

Kerr PJ; Eden JS; Di Giallonardo F; Peacock D; Liu J; Strive T; Read AF; Holmes EC, 2019, 'Punctuated evolution of myxoma virus: Rapid and disjunct evolution of a recent viral lineage in Australia', Journal of Virology, vol. 93, http://dx.doi.org/10.1128/JVI.01994-18

Koh C; Audsley MD; Di Giallonardo F; Kerton EJ; Young PR; Holmes EC; McGraw EA, 2019, 'Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture', Virus Evolution, vol. 5, http://dx.doi.org/10.1093/ve/vez012

Di Giallonardo F; Geoghegan JL; Cousins K; Shi M; Williamson JE; Holmes EC, 2018, 'Hidden diversity and evolution of viruses in market fish', Virus Evolution, vol. 4, pp. vey031 - vey031, http://dx.doi.org/10.1093/ve/vey031

Di Giallonardo F; Kok J; Fernandez M; Carter I; Geoghegan JL; Dwyer DE; Holmes EC; Eden JS, 2018, 'Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia', Viruses, vol. 10, http://dx.doi.org/10.3390/v10090476

Pinto AN; Hawke K; Castley A; Chibo D; Giallonardo FD; Cooper C; Sawleshwarkar S; Kelleher A; Dwyer DE, 2018, 'HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia', Future Virology, vol. 13, pp. 575 - 584, http://dx.doi.org/10.2217/fvl-2018-0031

Di Giallonardo F; Audsley MD; Shi M; Young PR; McGraw EA; Holmes EC, 2018, 'Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line', Journal of General Virology, vol. 99, pp. 832 - 836, http://dx.doi.org/10.1099/jgv.0.001079

Pinto A; Di Giallonardo F; Keen P; Cooper C; Telfer B; Cooper D; Grulich A; Kelleher A, 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, vol. 4, http://dx.doi.org/10.1093/ve/vey010.009

Giallonardo FD; Schlub TE; Shi M; Holmes EC, 2017, 'Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species', Journal of Virology, vol. 91, http://dx.doi.org/10.1128/JVI.02381-16

Wilson JAC; Prow NA; Schroder WA; Ellis JJ; Cumming HE; Gearing LJ; Poo YS; Taylor A; Hertzog PJ; Di Giallonardo F; Hueston L; Le Grand R; Tang B; Le TT; Gardner J; Mahalingam S; Roques P; Bird PI; Suhrbier A, 2017, 'RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation', PLoS Pathogens, vol. 13, http://dx.doi.org/10.1371/journal.ppat.1006155

Duchêne S; Duchêne DA; Di Giallonardo F; Eden JS; Geoghegan JL; Holt KE; Ho SYW; Holmes EC, 2016, 'Cross-validation to select Bayesian hierarchical models in phylogenetics', BMC Evolutionary Biology, vol. 16, http://dx.doi.org/10.1186/s12862-016-0688-y

Kok YL; Vongrad V; Shilaih M; Di Giallonardo F; Kuster H; Kouyos R; Günthard HF; Metzner KJ, 2016, 'Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4 + T cells', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep24157

Geoghegan JL; Senior AM; Giallonardo FD; Holmes EC, 2016, 'Virological factors that increase the transmissibility of emerging human viruses', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, pp. 4170 - 4175, http://dx.doi.org/10.1073/pnas.1521582113

Noguera-Julian M; Cozzi-Lepri A; Di Giallonardo F; Schuurman R; Däumer M; Aitken S; Ceccherini-Silberstein F; D'Arminio Monforte A; Geretti AM; Booth CL; Kaiser R; Michalik C; Jansen K; Masquelier B; Bellecave P; Kouyos RD; Castro E; Furrer H; Schultze A; Günthard HF; Brun-Vezinet F; Metzner KJ; Paredes R; Paredes R; Schuurman R; Günthard H; Reqaeui F; Kaiser R; Geretti AM; Brockmeyer N, 2016, 'Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants', Clinical Microbiology and Infection, vol. 22, pp. 191 - 200, http://dx.doi.org/10.1016/j.cmi.2015.10.004

Seifert D; Di Giallonardo F; Töpfer A; Singer J; Schmutz S; Günthard HF; Beerenwinkel N; Metzner KJ, 2016, 'A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations', Journal of Molecular Biology, vol. 428, pp. 238 - 250, http://dx.doi.org/10.1016/j.jmb.2015.12.012

St. John EP; Simen BB; Turenchalk GS; Braverman MS; Abbate I; Aerssens J; Bouchez O; Gabriel C; Izopet J; Meixenberger K; Di Giallonardo F; Schlapbach R; Paredes R; Sakwa J; Schmitz-Agheguian GG; Thielen A; Victor M; Metzner KJ; Däumer MP; Danzer M; Stabentheiner S; Pröll J; Hofer K; Mostmans W; Thys K; Van Marck H; Dubois M; Nicot F; Milan D; Thiele B; Kuecherer C; Nitsche A; Radonic A; Dabrowski PW; Lengauer T; Capobianchi MR; Bruselles A; Giombini E; Rozera G; Bartolini B; Codoñer FM; Pou C; Günthard HF; Yang WL; Aquino C; Bruggmann R; Künzli-Gontarczyk M; Stephens D; Makgamathe M; Khan G; Gordon M; Moreno E, 2016, 'A follow-up of the multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 ultra deep pyrosequencing', PLoS ONE, vol. 11, http://dx.doi.org/10.1371/journal.pone.0146687

Dill JA; Camus AC; Leary JH; Di Giallonardo F; Holmes EC; Nga TFF, 2016, 'Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of hepadnaviruses', Journal of Virology, vol. 90, pp. 7920 - 7933, http://dx.doi.org/10.1128/JVI.00832-16

di Giallonardo F; Geoghegan JL; Docherty DE; McLean RG; Zody MC; Qu J; Yang X; Birren BW; Malboeuf CM; Newman RM; Ip HS; Holmes EC, 2016, 'Fluid spatial dynamics of West Nile virus in the United States: Rapid spread in a permissive host environment', Journal of Virology, vol. 90, pp. 862 - 872, http://dx.doi.org/10.1128/JVI.02305-15

Duchene S; Di Giallonardo F; Holmes EC, 2016, 'Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales', Molecular Biology and Evolution, vol. 33, pp. 255 - 267, http://dx.doi.org/10.1093/molbev/msv207

Di Giallonardo F; Holmes EC, 2015, 'Exploring Host–Pathogen Interactions through Biological Control', PLoS Pathogens, vol. 11, http://dx.doi.org/10.1371/journal.ppat.1004865

Seifert D; Di Giallonardo F; Metzner KJ; Guenthard HF; Beerenwinkel N, 2015, 'A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory (vol 199, pg 191, 2014)', GENETICS, vol. 199, pp. 1271 - 1271, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000352734400028&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Cozzi-Lepri A; Noguera-Julian M; Di Giallonardo F; Schuurman R; Däumer M; Aitken S; Ceccherini-Silberstein F; Monforte ADA; Geretti AM; Booth CL; Kaiser R; Michalik C; Jansen K; Masquelier B; Bellecave P; Kouyos RD; Castro E; Furrer H; Schultze A; Günthard HF; Brun-Vezinet F; Paredes R; Metzner KJ; Brockmeyer N, 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, vol. 70, pp. 930 - 940, http://dx.doi.org/10.1093/jac/dku426

Di Giallonardo F; Holmes EC, 2015, 'Viral biocontrol: Grand experiments in disease emergence and evolution', Trends in Microbiology, vol. 23, pp. 83 - 90, http://dx.doi.org/10.1016/j.tim.2014.10.004

Seifert D; Giallonardo FD; Metzner KJ; Günthard HF; Beerenwinke N, 2015, 'A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory', Genetics, vol. 199, pp. 191 - 203, http://dx.doi.org/10.1534/genetics.114.172312

Di Giallonardo F; Töpfer A; Rey M; Prabhakaran S; Duport Y; Leemann C; Schmutz S; Campbell NK; Joos B; Lecca MR; Patrignani A; Däumer M; Beisel C; Rusert P; Trkola A; Günthard HF; Roth V; Beerenwinkel N; Metzner KJ, 2014, 'Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations', Nucleic Acids Research, vol. 42, http://dx.doi.org/10.1093/nar/gku537

Simen BB; Braverman MS; Abbate I; Aerssens J; Bidet Y; Bouchez O; Gabriel C; Izopet J; Kessler HH; Stelzl E; Di Giallonardo F; Schlapbach R; Radonic A; Paredes R; Recordon-Pinson P; Sakwa J; St. John EP; Schmitz-Agheguian GG; Metzner KJ; Däumer MP; Danzer M; Hackl C; Pröll J; Niklas N; Bizon B; Van Eygen V; Vandenbroucke I; Van Marck H; Dubois M; Nicot F; Milan D; Masquelier B; Fleury H; Viala S; Marell R; Thiele B; Kuecherer C; Meixenberger K; Nitsche A; Dabrowski PW; Ihlenfeldt HG; Capobianchi MR; Bruselles A; Rozera G; Bartolini B; Stephens D; Makgamathe M; Pillay D; Gordon M; Green T; Codoñer FM; Pou C; Günthard HF; Künzli-Gontarczyk M; Bruggmann R; Qi W; Turenchalk G; Hanczaruk B, 2014, 'An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing', Journal of Virological Methods, vol. 204, pp. 31 - 37, http://dx.doi.org/10.1016/j.jviromet.2014.04.007

Di Giallonardo F; Zagordi O; Duport Y; Leemann C; Joos B; Künzli-Gontarczyk M; Bruggmann R; Beerenwinkel N; Günthard HF; Metzner KJ, 2013, 'Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0074249

Decker M; Adamska M; Cronin A; Di Giallonardo F; Burgener J; Marowsky A; Falck JR; Morisseau C; Hammock BD; Gruzdev A; Zeldin DC; Arand M, 2012, 'EH3 (ABHD9): The first member of a new epoxide hydrolase family with high activity for fatty acid epoxides', Journal of Lipid Research, vol. 53, pp. 2038 - 2045, http://dx.doi.org/10.1194/jlr.M024448

Althaus CF; Vongrad V; Niederöst B; Joos B; Di Giallonardo F; Rieder P; Pavlovic J; Trkola A; Günthard HF; Metzner KJ; Fischer M, 2012, 'Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells', Retrovirology, vol. 9, http://dx.doi.org/10.1186/1742-4690-9-27

Metzner KJ; Leemann C; Di Giallonardo F; Grube C; Scherrer AU; Braun D; Kuster H; Weber R; Guenthard HF, 2011, 'Reappearance of minority K103N HIV-1 variants after interruption of ART initiated during primary HIV-1 infection', PLoS ONE, vol. 6, http://dx.doi.org/10.1371/journal.pone.0021734

Knoepfel SA; Di Giallonardo F; Däumer M; Thielen A; Metzner KJ, 2011, 'In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing', Journal of Virological Methods, vol. 171, pp. 329 - 338, http://dx.doi.org/10.1016/j.jviromet.2010.11.016

Huelsmann PM; Hofmann AD; Knoepfel SA; Popp J; Rauch P; Di Giallonardo F; Danke C; Gueckel E; Schambach A; Wolff H; Metzner KJ; Berens C, 2011, 'A suicide gene approach using the human pro-apoptotic protein tBid inhibits HIV-1 replication', BMC Biotechnology, vol. 11, http://dx.doi.org/10.1186/1472-6750-11-4


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