By Dr Ira William Deveson

Preprints

Suzuki K; Levert A; Yoo E; Matsuda M; Ishida T; Cysique L; Zaunders J; Deveson I; Barton K; Ode H; Iwatani Y; Brew B, 2026, Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Reduced Neuroaxonal Integrity, http://dx.doi.org/10.64898/2026.06.02.729658

Yeow D; Reis ALM; Stevanovski I; Njo N; Rudaks LI; Grosz BR; Sy JS; Kemp L; Chintalaphani SR; Chin M; Stoll M; Zhu D; Liang C; Morris K; Hannaford A; Shandiz E; Ahmad KE; El-Wahsh S; Reddel SW; Boland-Freitas R; Ghaoui R; Barnes S; Sturm J; Willard A; Jasinarachchi M; Hawke S; Simon NG; Worgan L; Manser D; Tchan M; Griffith NC; Davis RL; Fahey MC; Sue CM; McCombe PA; Ng K; Kennerson ML; Cheong PL; Kumar KR; Deveson IW, 2025, Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies, http://dx.doi.org/10.64898/2025.12.06.25340828

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 A; Figtree G; Deveson I; Siggs O, 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

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

Hanrahan B; Alreja K; Reis A; Chang K; Dissanayake DSB; Edwards R; Bertozzi T; Hammond J; O’Meally D; Deveson I; Georges A; Waters P; Patel H, 2024, A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies, http://dx.doi.org/10.1101/2024.09.05.611471

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

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, 2021, Advancing Quality-Control for NGS Measurement of Actionable Mutations in Circulating Tumor DNA, http://dx.doi.org/10.2139/ssrn.3830017

Deveson I; Madala BS; Blackburn J; Barker C; Wong T; Barton K; Smith M; Watkins N; Mercer T, 2018, Chiral DNA sequences as commutable reference standards for clinical genomics, http://dx.doi.org/10.1101/404285

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; group OS; 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, A CCG expansion in ABCD3 causes oculopharyngodistal myopathy in individuals of European ancestry, http://dx.doi.org/10.1101/2023.10.09.23296582

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

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, A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps, http://dx.doi.org/10.1101/2025.05.01.651798

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

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/10.1101/2021.04.06.438497

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

Foster CSP; Stelzer-Braid S; Deveson IW; Bull RA; Yeang M; Phan-Au J; Silva MR; van Hal SJ; Rockett RJ; Sintchenko V; Kim KW; Rawlinson WD, Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia, http://dx.doi.org/10.1101/2021.08.19.21262296

Samarasinghe S; Deveson I; Gamaarachchi H, Base modification analysis in long read sequencing data using Minimod, http://dx.doi.org/10.1101/2025.07.16.665072

Maduranga S; Valencia BM; Sigera C; Weeratunga P; Fernando D; Rajapakse S; Rapadas M; Deveson IW; Lloyd AR; Bull R; Rodrigo C, Between- and within-host mutation of dengue virus, http://dx.doi.org/10.1101/2025.10.12.680595

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, 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

Stewart N; Henden N; Smith-Diaz C; Rigby J; Butters A; Baker A; Catto L; Subasinghe I; Yeates L; Geraghty L; Follett J; Sillence D; Kemp L; Deveson IW; Alasady M; Wilson S; Simons C; MacArthur DG; Gray B; Duflou J; Freckmann M-L; Richardson E; Zankl A; Ingles J, Cardiomyopathy and sudden cardiac death as a rare presentation of mucolipidosis type III in a family with compound heterozygous variants in GNPTAB, http://dx.doi.org/10.21203/rs.3.rs-8674450/v1

Madala BS; Reis ALM; Deveson IW; Rawlinson W; Mercer TR, 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

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

Angeloni A; Hammond JM; Peters TJ; Reis ALM; Kemp L; Amos T; Gamaarachchi H; Humphries S; Wilmott LA; Pal S; Masamsetti VP; Weatherstone M; Ip KCK; Pazaky K; Steel A; Lyons R; Walters ED; Liu N; Tam P; Polo JM; Waters P; Clark SJ; Richards LJ; Smith AD; Lee H; Deveson IW; Griffith OW; Skvortsova K, DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage, http://dx.doi.org/10.1101/2025.11.09.686659

Skvortsova K; Angeloni A; Hammond J; Peters T; Reis ALM; Kemp L; Amos T; Gamaarachchi H; Humphries S; Wilmott L; Pal S; Masamsetti VP; Weatherstone M; Ip KCK; Pazaky K; Steel A; Lyons R; Walters E; Liu N; Tam P; Polo J; Waters P; Clark S; Richards L; Smith A; Lee H; Deveson I; Griffith O, DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage, http://dx.doi.org/10.21203/rs.3.rs-8110586/v1

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

Martin EM; Harris M; Stait T; Casauria S; Pierini E; White SM; Hermes A; McGaughran J; Rius R; MacArthur DG; Lassmann T; Richmond C; Smith J; Wallis M; Sallevelt S; Field M; Cunningham C; Stroud DA; Sadedin S; Dudding-Byth T; Cooper S; Goranitis I; Deveson IW; LeBlanc S; Walsh M; Bodek S; Fennell AP; Krzesinski E; Jelenich S; Madelli EO; Austin R; Pysar R; Thompson H; Cilento L; Dreyer L; Wilkins EJ; Lynch E; Carr M; Zurita E; Broadbent J; Kooshavar D; Wedd L; Zhang E; Zhao T; Gray C; Formaini E; Hajjari M; Richards C; Gonzalez FS; Simons C; Boughtwood T; Palmer EE; Tan TY; Baynam G; Christodoulou J, Establishing The Australian Undiagnosed Disease Network (UDN-Aus); Australia’s first national rare disease diagnostic network, http://dx.doi.org/10.21203/rs.3.rs-8091344/v1

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; S C; Tangye SG; Di Sabatino A; Lenti MV; Pasini A; Ciccocioppo R; Ahlenstiel G; Suan D; Tye-Din JA; Goodnow CC; Luciani F, Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease, http://dx.doi.org/10.1101/2024.03.17.24304320

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

Samarakoon H; Ferguson JM; Jenner SP; Amos TG; Parameswaran S; Gamaarachchi H; Deveson IW, Flexible and efficient handling of nanopore sequencing signal data with slow5tools, http://dx.doi.org/10.1101/2022.06.19.496732

González-Rajal Á; D’Araujo TY; Ovchinnikov V; Alcalá JLG-J; Wang T; Lausen B; Brethouwer T; Angeloni A; Ross SE; Burgos-Ruiz AM; Álvarez-Presas M; Mota-Gómez I; Acemel RD; Harris RJ; Loi-Luu P; Jimenez GE; Daners A; Ferguson JM; Hammond JM; Gamaarachchi H; Degnan BM; Degnan SM; Mackay JP; Undheim EAB; Ruiz-Trillo I; Clark SJ; Tena JJ; Lupiáñez DG; Church SH; Dunn CW; Marletaz F; Deveson IW; Cummins SF; Neely GG; de Mendoza A; Bogdanovic O, Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity, http://dx.doi.org/10.64898/2026.08.01.742136

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

Ferguson JM; Gamaarachchi H; Nguyen T; Gollon A; Tong S; Aquilina-Reid C; Bowen-James R; Deveson IW, InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses, http://dx.doi.org/10.1101/2021.04.21.440861

Williams TC; Kroukamp H; Xu X; Wightman ELI; Llorente B; Borneman AR; Carpenter AC; Van Wyk N; Espinosa MI; Daniel EL; Walker RSK; Cai Y; Nevalainen HKM; Curach NC; Deveson IW; Mercer TR; Johnson DL; Mitchell LA; Bader JS; Stracquadanio G; Boeke JD; Goold HD; Pretorius IS; Paulsen IT, Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements, http://dx.doi.org/10.1101/2022.07.22.501046

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

Smits N; Rasmussen J; Bodea GO; Amarilla AA; Gerdes P; Sanchez-Luque FJ; Ajjikuttira P; Modhiran N; Liang B; Faivre J; Deveson IW; Khromykh AA; Watterson D; Ewing AD; Faulkner GJ, 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

Wong B; Singh G; Javaid H; Denolf K; Liyanage K; Samarakoon H; Deveson IW; Gamarachchi H, Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish, http://dx.doi.org/10.64898/2026.03.25.714356

Danzi MC; Xu IRL; Fazal S; Dolzhenko E; Pellerin D; Weisburd B; Van de Vondel L; Reuter C; Sampson JB; Folland C; Scriba CK; Monahan G; Lamont PJ; Wertz J; Rebelo A; Gibson SB; Calame DG; Rafehi H; Snell P; Kotschet K; Davies KC; Stevanovski I; Deveson IW; Miller DE; Wei C-L; Grimwood J; Muzny DM; Lennon N; Bahlo M; Lockhart PJ; Wheeler M; O’Donnell-Luria A; Wuchty S; Ravenscroft G; Eberle MA; Garimella KV; Sedlazeck FJ; Talkowski ME; Schatz MC; Eichler EE; Group AOURPLRW; Zuchner S, Population-scale variability at short tandem repeat loci reveals pathogenicity signature, http://dx.doi.org/10.1101/2025.01.06.631535

Smith-Diaz CC; Iaprintsev V; Huckstep H; Macciocca I; Piers AT; Henden N; Bryen S; Stewart N; Butters A; Baker AM; Catto L; Kemp L; King I; Le LHH; Elliott DA; Watt KI; Mathew J; Justo R; Richardson E; Simons C; Landstrom AP; Theodoris CV; Deveson IW; MacArthur DG; Konstantinov IE; Weintraub RG; Porrello ER; Humphrey SJ; Ingles J, Proteomics Uncovers Cryptic JPH2 Loss in Paediatric Dilated Cardiomyopathy, http://dx.doi.org/10.64898/2026.06.16.26355718

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

Kim KW; Deveson IW; Pang CNI; Yeang M; Naing Z; Adikari T; Hammond JM; Stevanovski I; Beukers AG; Verich A; Yin S; McFarlane D; Wilkins MR; Stelzer-Braid S; Bull RA; Craig ME; Hal SJV; Rawlinson WD, Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing, http://dx.doi.org/10.21203/rs.3.rs-105996/v1

Forkgen J; Masle-Farquhar E; Fontaine Y; Russell A; Ji S; Peters TJ; Qiao Z; Geaghan M; Jackson KJ; Hammond JM; Deveson IW; David C; Lemberg DA; Gupta N; Fuentes-Bolanos N; Mustjoki S; Hwa V; Tangye SG; Gray PE; Siggs OM, Sequential mosaic variants in KRAS and STAT5B associated with a mixed phenotype of two acquired errors of immunity, http://dx.doi.org/10.1101/2024.08.07.24311150

Hanrahan BJ; Chang JK; Milton AM; Lister NC; Dissanayake DSB; Hammond JM; Reis ALM; Deveson IW; Ruiz-Herrera A; Patel HR; Graves JAM; Georges A; Waters PD, 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

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

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, 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; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis, http://dx.doi.org/10.21203/rs.3.rs-668517/v1

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; Porcel LM; Seilhean D; Zuchner S; Durr A; Brais B, 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

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

Wong B; Ferguson JM; Gamaarachchi H; Deveson IW, Streamlining remote nanopore data access with slow5curl, http://dx.doi.org/10.1101/2023.11.28.569128

Gudkov M; Reis ALM; Kumaheri M; Deveson IW, SVlog: a logic programming framework for understanding structural variation in genomic disease, http://dx.doi.org/10.64898/2026.08.11.744322

Tanudisastro HA; Cuomo ASE; Weisburd B; Welland M; Spenceley E; Franklin M; Xue A; Huang HL; Bowen B; Fan J; Dong OA; Henry A; Allen PC; Wing K; Tang O; Gray M; Reis ALM; Margoliash J; Kurtas NE; Pullin JM; Lee AS; Brand H; Harper M; Bobowik K; Silk M; Miniter A; Marshall J; Bakiris V; Madala BS; Uren C; Bartie C; McCloy RA; 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, Tandem repeat variation shapes immune cell type-specific gene expression, http://dx.doi.org/10.1101/2024.11.02.621562

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

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