By Dr Ira William Deveson

Preprints

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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