By Dr Ira William Deveson

Preprints

Grosz BR; Parmar JM; Ellis M; Bryen S; Simons C; Reis ALM; Stevanovski I; Deveson IW; Nicholson G; Laing N; Wallis M; Ravenscroft G; Kumar KR; Vucic S; Kennerson ML, 2024, A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing, , http://dx.doi.org/10.1101/2024.04.22.24306048

Singh M; Louie RHY; Samir J; Field MA; Milthorpe C; Aldiriki T; Mackie J; Roper E; Faulks M; Jackson KJL; Calcino A; Hardy MY; Blombery P; Amos TG; Deveson IW; Read SA; Shek D; Guerin A; Ma CS; Tangye SG; Sabatino AD; Lenti MV; Pasini A; Ciccocioppo R; Ahlenstiel G; Suan D; Tye-Din JA; Goodnow CC; Luciani F, 2024, Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease, , http://dx.doi.org/10.1101/2024.03.17.24304320

Samarakoon H; Liyanage K; Ferguson J; Parameswaran S; Gamaarachchi H; Deveson I, 2024, Interactive visualisation of raw nanopore signal data with Squigualiser, , http://dx.doi.org/10.1101/2024.02.19.581111

Reis ALM; Rapadas M; Hammond JM; Gamaarachchi H; Stevanovski I; Kumaheri MA; Chintalaphani SR; Dissanayake DSB; Siggs OM; Hewitt AW; Llamas B; Brown A; Baynam G; Mann GJ; Hermes A; Patel HR; Deveson IW, 2023, The landscape of genomic structural variation in Indigenous Australians, , http://dx.doi.org/10.1101/2023.10.17.562810

Cortese A; Beecroft SJ; Facchini S; Curro R; Cabrera-Serrano M; Stevanovski I; Chintalaphani S; Gamaarachchi H; Weisburd B; Folland C; Monahan G; Scriba CK; Dofash L; Johari M; Grosz BR; Ellis M; Fearnley LG; Tankard R; Read J; Bahlo M; Merve A; Dominik N; Vegezzi E; Schnekenberg RP; Fernandez G; Masingue M; Giovannini D; Delatycki M; Storey E; Gardner M; Amor D; Nicholson G; Vucic S; Henderson RD; Robertson T; Dyke J; Fabian V; Mastaglia F; Davis MR; Kennerson M; England G; Quinlivan R; Hammans S; Tucci A; McLean CA; Laing NG; Stojkovic T; Houlden H; Hanna MG; Deveson I; Lockhart PJ; Lamont PJ; Fahey MC; Bugiardini E; Ravenscroft G, 2023, A CCG expansion inABCD3causes oculopharyngodistal myopathy in individuals of European ancestry, , http://dx.doi.org/10.1101/2023.10.09.23296582

Mallawaarachchi A; Hort Y; Sullivan P; Wedd L; Fowles L; Stevanonvski I; Deveson I; Simons C; Mallett A; Patel C; Furlong T; Cowley M; Shine J, 2023, Short and long-read whole genome sequencing explains most undiagnosed Autosomal Dominant Polycystic Kidney Disease, , http://dx.doi.org/10.21203/rs.3.rs-2397081/v1

Samarakoon H; Ferguson J; Gamaarachchi H; Deveson I, 2023, Accelerated nanopore basecalling with SLOW5 data format, , http://dx.doi.org/10.1101/2023.02.06.527365

Hanrahan B; Chang K; Lister N; Dissanayake DSB; Hammond J; Reis ALM; Deveson I; Ruiz-Herrera A; Patel H; Marshall Graves J; Georges A; Waters P, 2023, Both phenotypic and genotypic sex influence sex chromosome dosage compensation in a sex reversing lizard, , http://dx.doi.org/10.1101/2023.08.24.554710

Angeloni A; Fissette S; Kaya D; Hammond J; Gamaarachchi H; Deveson I; Klose R; Li W; Zhang X; Bogdanovic O, 2023, Extensive DNA methylome rearrangement during early lamprey embryogenesis, , http://dx.doi.org/10.1101/2023.05.25.542242

Gamaarachchi H; Ferguson J; Samarakoon H; Liyanage K; Deveson I, 2023, Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters, , http://dx.doi.org/10.1101/2023.05.09.539953

Wong B; Ferguson J; Gamaarachchi H; Deveson I, 2023, Streamlining remote nanopore data access withslow5curl, , http://dx.doi.org/10.1101/2023.11.28.569128

Louie R; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire H; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2022, CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion, , http://dx.doi.org/10.21203/rs.3.rs-1495587/v1

Louie RHY; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire HM; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2022, CAR⁺ and CAR^- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion, , http://dx.doi.org/10.1101/2022.03.29.22273013

Samarakoon H; Ferguson J; Jenner S; Amos T; Parameswaran S; Gamaarachchi H; Deveson I, 2022, Flexible and efficient handling of nanopore sequencing signal data with slow5tools, , http://dx.doi.org/10.1101/2022.06.19.496732

Williams T; Kroukamp H; Xu X; Wightman E; Llorente B; Borneman A; Carpenter A; Van Wyk N; Espinosa M; Daniel E; Walker R; Cai Y; Nevalainen H; Curach N; Deveson I; Mercer T; Johnson D; Mitchell L; Bader J; Stracquadanio G; Boeke J; Goold H; Pretorius I; Paulsen I, 2022, Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements, , http://dx.doi.org/10.1101/2022.07.22.501046

Willey J; Morrison T; Austermiller B; Crawford E; Craig D; Blomquist T; Jones W; Wali A; Lococo J; Haseley N; Richmond T; Novoradovskaya N; Kusko R; Chen G; Li Q-Z; Johann D; Deveson I; Mercer T; Wu L; Xu J, 2021, Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA, , http://dx.doi.org/10.1101/2021.04.06.438497

Stevanovski I; Chintalaphani S; Gamaarachchi H; Ferguson J; Pineda S; Scriba C; Tchan M; Fung V; Ng K; Cortese A; Houlden H; Dobson-Stone C; Fitzpatrick L; Halliday G; Ravenscroft G; Davis M; Laing N; Fellner A; Kennerson M; Kumar K; Deveson I, 2021, Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing, , http://dx.doi.org/10.1101/2021.09.27.21263187

Tennant E; Figtree M; Tallon J; Bull R; Yeang M; Deveson I; Ferguson J; Adikari T; Holmes E; Hal SV; Hammond J; Stevanovski I; Mitsakos K; Hilditch-Roberts D; Rawlinson W; Hudson B, 2021, Epidemiological and Genomic analysis of a Sydney Hospital COVID-19 Outbreak, , http://dx.doi.org/10.1101/2021.02.17.21251943

Smits N; Rasmussen J; Bodea G; Amarilla A; Gerdes P; Sanchez-Luque F; Ajjikuttira P; Modhiran N; Liang B; Faivre J; Deveson I; Khromykh A; Watterson D; Ewing A; Faulkner G, 2021, No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing, , http://dx.doi.org/10.1101/2021.05.28.446065

Reis AM; Hammond J; Stevanovski I; Arnold J; McGregor I; Deveson I; Gururajan A, 2021, Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition, , http://dx.doi.org/10.1101/2021.11.25.468910

Bull R; Adikari T; Ferguson J; Hammond J; Stevanovski I; Beukers A; Naing Z; Yeang M; Verich A; Gamaarachchi H; Kim KW; Luciani F; Stelzer-Braid S; Eden J-S; Rawlinson W; van Hal S; Deveson I, 2020, Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis, , http://dx.doi.org/10.1101/2020.08.04.236893

Madala BS; Reis A; Deveson I; Rawlinson W; Mercer T, 2020, Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests, , http://dx.doi.org/10.1101/2020.06.09.143412

Deveson I; Brunck M; Blackburn J; Tseng E; Hon T; Clark T; Clark M; Crawford J; Dinger M; Nielsen L; Mattick J; Mercer T, 2017, Universal alternative splicing of noncoding exons, , http://dx.doi.org/10.1101/136275

Willey JC; Morrison T; Austermiller B; Crawford EL; Craig DJ; Blomquist TM; Jones WD; Wali A; Lococo JS; Haseley N; Richmond TA; Novoradovskaya N; Kusko R; Chen G; Li Q-Z; Johann D; Deveson IW; Mercer T; Wu L; Xu J, Advancing Quality-Control for NGS Measurement of Actionable Mutations in Circulating Tumor DNA, , http://dx.doi.org/10.2139/ssrn.3830017

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