By Dr Ira William Deveson

Preprints

Fontaine Y; Aradhya S; Ji S; Masle-Farquhar E; Bosi I; Forkgen J; Qiao Z; Stevanovski I; Reis ALM; Rapadas M; Suan D; Hsu P; Wainstein B; Hewitt AW; Figtree GA; Deveson IW; Siggs OM, 2025, Combined genomic and phenotypic classification of inherited and acquired genetic disease with long-read sequencing, http://dx.doi.org/10.1101/2025.05.08.25327265

Patel HR; Alreja K; Reis ALM; Chang JK; Chew ZA; Jung H; Hammond JM; Deveson IW; Ruiz-Herrera A; Marin-Gual L; Holleley CE; Zhang X; Lister NC; Whiteley S; Xiong L; Dissanayake DSB; Waters PD; Georges A, 2025, A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragonPogona vitticeps, http://dx.doi.org/10.1101/2025.05.01.651798

Tanudisastro HA; Cuomo ASE; Weisburd B; Welland M; Spenceley E; Franklin M; Xue A; Bowen B; Wing K; Tang O; Gray M; Reis ALM; Margoliash J; Kurtas NE; Pullin JM; Lee AS; Brand H; Harper M; Bobowik K; Silk M; Marshall J; Bakiris V; Madala BS; Uren C; Bartie C; Senabouth A; Dashnow H; Fearnley L; Martin-Trujillo A; Dolzhenko E; Qiao Z; Grieve SM; Nguyen T; Ben-David E; Chen L; Farh KK-H; Talkowski M; Alexander SI; Siggs OM; Gruenschloss L; Nicholas HR; Piscionere J; Simons C; Wallace C; Gymrek M; Deveson IW; Hewitt AW; Figtree GA; de Lange KM; Powell JE; MacArthur DG, 2025, Polymorphic tandem repeats influence cell type-specific gene expression across the human immune landscape., http://dx.doi.org/10.1101/2024.11.02.621562

Gamaarachchi H; Stevanovski I; Hammond JM; Reis ALM; Rapadas M; Jayasooriya K; Russell T; Yeow D; Hort Y; Mallett AJ; Stackpoole E; Roman L; Silver LW; Hogg CJ; Streeting L; Bogdanovic O; Rodrigues R; Nascimento L; Cardoso AL; Georges A; Cheng H; Patel HR; Kumar KR; Mallawaarachchi AC; Deveson IW, 2025, Adaptively integrated sequencing and assembly of near-complete genomes, http://dx.doi.org/10.1101/2025.03.31.646505

Samarasinghe S; Deveson I; Gamaarachchi H, 2025, Realfreq: Real-time base modification analysis for nanopore sequencing, http://dx.doi.org/10.1101/2025.01.23.634192

Hanrahan BJ; Alreja K; Reis ALM; Chang JK; Dissanayake DSB; Edwards RJ; Bertozzi T; Hammond JM; O’Meally D; Deveson IW; Georges A; Waters P; Patel HR, 2024, A genome assembly and annotation for the Australian alpine skinkBassiana duperreyiusing long-read technologies, http://dx.doi.org/10.1101/2024.09.05.611471

Forkgen J; Masle-Farquhar E; Fontaine Y; Russell A; Ji S; Peters TJ; Qiao Z; Geaghan M; Jackson KJL; Hammond JM; Deveson IW; David C; Lemberg DA; Gupta N; Fuentes-Bolanos N; Mustjoki S; Hwa V; Tangye SG; Gray PE; Siggs OM, 2024, Sequential mosaic variants inKRASandSTAT5Bassociated with a mixed phenotype of two acquired errors of immunity, http://dx.doi.org/10.1101/2024.08.07.24311150

Pellerin D; Méreaux J-L; Boluda S; Danzi MC; Dicaire M-J; Davoine C-S; Genis D; Spurdens G; Ashton C; Hammond JM; Gerhart BJ; Chelban V; Le PU; Safisamghabadi M; Yanick C; Lee H; Nageshwaran SK; Matos-Rodrigues G; Jaunmuktane Z; Petrecca K; Akbarian S; Nussenzweig A; Usdin K; Renaud M; Bonnet C; Ravenscroft G; Saporta MA; Napierala JS; Houlden H; Deveson IW; Napierala M; Brice A; Molina Porcel L; Seilhean D; Zuchner S; Durr A; Brais B, 2024, Somatic instability of the FGF14 -SCA27B GAA•TTC repeat reveals a marked expansion bias in the cerebellum., http://dx.doi.org/10.1101/2024.07.01.24309777

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

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

Jayasooriya K; Jenner S; Marasinghe P; Senanayake U; Saadat H; Taubman D; Ragel R; Gamaarachchi H; Deveson I, 2024, A new compression strategy to reduce the size of nanopore sequencing data, http://dx.doi.org/10.1101/2024.10.02.616377

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

Samarakoon H; Wan YK; Parameswaran S; Göke J; Gamaarachchi H; Deveson I, 2024, Leveraging Basecaller’s Move Table to Generate a Lightweight k-mer Model, http://dx.doi.org/10.1101/2024.06.30.601452

Rudaks LI; Stevanovski I; Yeow D; Reis A; Chintalaphani S; Cheong PL; Gamaarachchi H; Worgan L; Ahmad K; Hayes M; Hannaford A; Kim S; Fung V; Halmagyi M; Martin A; Manser D; Tchan M; Ng K; Kennerson M; Deveson I; Kumar KR, 2024, Targeted long-read sequencing as a single assay improves diagnosis of spastic-ataxia disorders, http://dx.doi.org/10.1101/2024.09.04.24312938

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

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

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

Hanrahan B; Chang K; Milton A; Lister N; Dissanayake DSB; Hammond J; Reis ALM; Deveson I; Ruiz-Herrera A; Patel H; Graves JM; Georges A; Waters P, 2023, Sex chromosome dosage compensation in a sex reversing skink is not influenced by sexual phenotype, http://dx.doi.org/10.1101/2023.08.24.554710

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

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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