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2023
Dusadeepong R, Delvallez G, Cheng S, Meng S, Sreng N, Letchford J, Choun K, Teav S, Hardy L, Jacobs J, Hoang T, Seemann T, Howden BP, Glaser P, Stinear TP, Vandelannoote K.
Microb Genom. 2023 Mar;9(3). doi: 10.1099/mgen.0.000972.
PMID: 36961484
Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink.
Porter AF, Purcell DFJ, Howden BP, Duchene S.
Virus Evol. 2023 Jan 10;9(1):vead002. doi: 10.1093/ve/vead002. eCollection 2023.
PMID: 36751428
An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance.
Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, Seemann T.
Nat Commun. 2023 Jan 4;14(1):60. doi: 10.1038/s41467-022-35713-4.
PMID: 36599823
Donnan EJ, Marais BJ, Coulter C, Waring J, Bastian I, Williamson DA, Sherry NL, Bond K, Sintchenko V, Meumann EM, Horan K, Cooley L, Denholm JT.
Commun Dis Intell (2018). 2023 Feb 28;47. doi: 10.33321/cdi.2023.47.8.
PMID: 36850064
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2022
George AM, Wille M, Wang J, Anderson K, Cohen S, Moselen J, Lee LYY, Suen WW, Bingham J, Dalziel AE, Whitney P, Stannard H, Hurt AC, Williams DT, Deng YM, Barr IG.
Virology. 2022 Nov;576:117-126. doi: 10.1016/j.virol.2022.09.001. Epub 2022 Sep 21.
PMID: 36228351
Global disparities in SARS-CoV-2 genomic surveillance.
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveillance Network; GISAID core curation team; Network for Genomic Surveillance in South Africa (NGS-SA); Swiss SARS-CoV-2 Sequencing Consortium, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR.
Nat Commun. 2022 Nov 16;13(1):7003. doi: 10.1038/s41467-022-33713-y.
PMID: 36385137 Free PMC article.
Sikorski MJ, Hazen TH, Desai SN, Nimarota-Brown S, Tupua S, Sialeipata M, Rambocus S, Ingle DJ, Duchene S, Ballard SA, Valcanis M, Zufan S, Ma J, Sahl JW, Maes M, Dougan G, Thomsen RE, Robins-Browne RM, Howden BP, Naseri TK, Levine MM, Rasko DA.
mBio. 2022 Oct 26;13(5):e0192022. doi: 10.1128/mbio.01920-22. Epub 2022 Sep 12.
PMID: 36094088 Free PMC article.
Sikorski MJ, Ma J, Hazen TH, Desai SN, Tupua S, Nimarota-Brown S, Sialeipata M, Rambocus S, Ballard SA, Valcanis M, Thomsen RE, Robins-Browne RM, Howden BP, Naseri TK, Levine MM, Rasko DA.
PLoS Negl Trop Dis. 2022 Oct 17;16(10):e0010348. doi: 10.1371/journal.pntd.0010348. eCollection 2022 Oct.
PMID: 36251704 Free PMC article.
Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl.
Wille M, Tolf C, Latorre-Margalef N, Fouchier RAM, Halpin RA, Wentworth DE, Ragwani J, Pybus OG, Olsen B, Waldenström J.
Virus Evol. 2022 Aug 27;8(2):veac074. doi: 10.1093/ve/veac074. eCollection 2022.
PMID: 36128050 Free PMC article.
Dale K, Globan M, Horan K, Sherry N, Ballard S, Tay EL, Bittmann S, Meagher N, Price DJ, Howden BP, Williamson DA, Denholm J.
Lancet Reg Health West Pac. 2022 Aug 18;28:100556. doi: 10.1016/j.lanwpc.2022.100556. eCollection 2022 Nov.
PMID: 36034164 Free PMC article.
Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016.
Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA.
Lancet Reg Health West Pac. 2022 Jun 16;24:100488. doi: 10.1016/j.lanwpc.2022.100488. eCollection 2022 Jul.
PMID: 35769175 Free PMC article.
Australia as a global sink for the genetic diversity of avian influenza A virus.
Wille M, Grillo V, Ban de Gouvea Pedroso S, Burgess GW, Crawley A, Dickason C, Hansbro PM, Hoque MA, Horwood PF, Kirkland PD, Kung NY, Lynch SE, Martin S, McArthur M, O'Riley K, Read AJ, Warner S, Hoye BJ, Lisovski S, Leen T, Hurt AC, Butler J, Broz I, Davies KR, Mileto P, Neave MJ, Stevens V, Breed AC, Lam TTY, Holmes EC, Klaassen M, Wong FYK.
PLoS Pathog. 2022 May 10;18(5):e1010150. doi: 10.1371/journal.ppat.1010150. eCollection 2022 May.
PMID: 35536868 Free PMC article.
Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea.
Palou T, Wilmot M, Duchene S, Porter A, Kemoi J, Suarkia D, Andersson P, Watt A, Sherry N, Seemann T, Sait M, Turharus C, Nguyen S, Schlebusch S, Thompson C, McMahon J, Vaccher S, Lin C, Esoram D, Howden BP, Susapu M.
Virus Evol. 2022 Apr 7;8(1):veac033. doi: 10.1093/ve/veac033. eCollection 2022 Apr.
PMID: 35875697 Free PMC article.
AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic.
Hoang T, da Silva AG, Jennison AV, Williamson DA, Howden BP, Seemann T.
Nat Commun. 2022 Feb 14;13(1):865. doi: 10.1038/s41467-022-28529-9.
PMID: 35165271 Free PMC article.
Higgs C, Sherry NL, Seemann T, Horan K, Walpola H, Kinsella P, Bond K, Williamson DA, Marshall C, Kwong JC, Grayson ML, Stinear TP, Gorrie CL, Howden BP.
Nat Commun. 2022 Jan 26;13(1):509. doi: 10.1038/s41467-022-28156-4.
PMID: 35082278 Free PMC article
Towards Equitable Access to Public Health Pathogen Genomics in the Western Pacific.
Lin C, da Silva E, Sahukhan A, Palou T, Buadromo E, Hoang T, Howden BP.
Lancet Reg Health West Pac. 2022 Jan;18:100321. doi: 10.1016/j.lanwpc.2021.100321. Epub 2021 Nov 24.
PMID: 34841379 Free PMC article. Review
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2021
Gorrie CL, Da Silva AG, Ingle DJ, Higgs C, Seemann T, Stinear TP, Williamson DA, Kwong JC, Grayson ML, Sherry NL, Howden BP.
Lancet Microbe. 2021 Nov;2(11):e575-e583. doi: 10.1016/S2666-5247(21)00149-X. Epub 2021 Aug 6.
PMID: 35544081
Lane CR, Sherry NL, Porter AF, Duchene S, Horan K, Andersson P, Wilmot M, Turner A, Dougall S, Johnson SA, Sait M, Gonçalves da Silva A, Ballard SA, Hoang T, Stinear TP, Caly L, Sintchenko V, Graham R, McMahon J, Smith D, Leong LE, Meumann EM, Cooley L, Schwessinger B, Rawlinson W, van Hal SJ, Stephens N, Catton M, Looker C, Crouch S, Sutton B, Alpren C, Williamson DA, Seemann T, Howden BP.
Lancet Public Health. 2021 Aug;6(8):e547-e556. doi: 10.1016/S2468-2667(21)00133-X. Epub 2021 Jul 10.
PMID: 34252365 Free PMC article.
Tuberculosis in Australia's tropical north: a population-based genomic epidemiological study.
Meumann EM, Horan K, Ralph AP, Farmer B, Globan M, Stephenson E, Popple T, Boyd R, Kaestli M, Seemann T, Vandelannoote K, Lowbridge C, Baird RW, Stinear TP, Williamson DA, Currie BJ, Krause VL.
Lancet Reg Health West Pac. 2021 Jul 31;15:100229. doi: 10.1016/j.lanwpc.2021.100229. eCollection 2021 Oct.
PMID: 34528010 Free PMC article.
An implementation science approach to evaluating pathogen whole genome sequencing in public health.
Ferdinand AS, Kelaher M, Lane CR, da Silva AG, Sherry NL, Ballard SA, Andersson P, Hoang T, Denholm JT, Easton M, Howden BP, Williamson DA.
Genome Med. 2021 Jul 28;13(1):121. doi: 10.1186/s13073-021-00934-7.
PMID: 34321076 Free PMC article.
Luo T, Xu P, Zhang Y, Porter JL, Ghanem M, Liu Q, Jiang Y, Li J, Miao Q, Hu B, Howden BP, Fyfe JAM, Globan M, He W, He P, Wang Y, Liu H, Takiff HE, Zhao Y, Chen X, Pan Q, Behr MA, Stinear TP, Gao Q.
Nat Commun. 2021 May 3;12(1):2491. doi: 10.1038/s41467-021-22760-6.
PMID: 33941780 Free PMC article.
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2020
Complete microbial genomes for public health in Australia and the Southwest Pacific.
Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, Sintchenko V, Wang Q, Rockett RJ, Timms VJ, Martinez E, Ballard S, Tomita T, Isles N, Horan KA, Pitchers W, Stinear TP, Williamson DA, Howden BP, Seemann T, Communicable Diseases Genomics Network Cdgn.
Microb Genom. 2020 Dec;6(12):mgen000471. doi: 10.1099/mgen.0.000471. Epub 2020 Nov 12.
PMID: 33180013 Free PMC article.