By Dr Ira William Deveson

Conference Papers

Siggs O; Schmidt J; Ji S; Deveson I; Kuot A; Fogarty R; Leonardos L; Dimasi D; Craig J, 2023, 'Intronic tandem repeat expansion in TMCO1 is associated with open angle glaucoma severity', in CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY, WILEY, pp. 918 - 918

Louie R; Cai C; Balraj V; Singh M; Jackson K; Deveson I; Ferguson J; Amos T; Gowrishankar K; Bishop D; Blyth E; Gottlieb D; Micklethwaite K; Luciani F, 2021, 'Single cell multi-omics identifies evolving phenotypes of CAR CD19 and endogenous T cell clones', in EUROPEAN JOURNAL OF IMMUNOLOGY, WILEY, pp. 412 - 412, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000753366402197&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Abstracts

Louie RY; Samir J; Cai C; McGuire H; Amos T; Fergsuson J; Deveson I; Adikari T; Bonomi M; Bishop D; Mason CE; Balderas R; Ruella M; Singh M; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2024, 'Abstract 882: Harnessing single cell multi-omics data to identify predictors of clinical outcome in CD19 CAR T cell therapy', in Cancer Research, American Association for Cancer Research (AACR), Vol. 84, pp. 882 - 882, http://dx.doi.org/10.1158/1538-7445.am2024-882

Laing N; Kennerson M; Lamont P; Vucic S; Davis M; Bryson-Richardson R; Ravenscroft G; Perez-Siles G; Ghaoui R; Narayanan R; McCombe P; Deveson I; Bryen S; Grosz B; Johari M; Rick A; Folland C; Scriba C; Parmar J; Ellis M, 2024, '482P Closing the gap in diagnosis of neuropathies and late-onset neurological disorders – a trans-Australia collaboration', in Neuromuscular Disorders, Elsevier BV, Vol. 43, pp. 104441.319 - 104441.319, http://dx.doi.org/10.1016/j.nmd.2024.07.328

Rudaks LI; Yeow D; Chintalaphani S; Stevanovski I; Reis AL; Fung VS; Hayes M; Ahmad K; Worgan L; Tchan M; Ng K; Kennerson ML; Cheong PL; Deveson I; Kumar KR, 2024, '6 SCA27B identified as a common cause of unsolved ataxia in a cohort evaluated with long-read sequencing', BMJ, pp. a3.1 - a3a3, presented at Young Investigators Session Abstracts, http://dx.doi.org/10.1136/bmjno-2024-anzan.6

French HJ; Anderson S; Deveson IW; Stevanovski I; Nelson A; Matthews S; Gou M; Cheong PL; Trent RJ; Ho PJ, 2022, 'Characterising complex rearrangements with long-read sequencing in thalassaemia', in Pathology, Elsevier BV, Vol. 54, pp. S73 - S74, http://dx.doi.org/10.1016/j.pathol.2021.12.242

Olivé M; Stevanovski I; Quereda LG; Morris G; Segarra-Casas A; Rodriguez-Santiago B; Gallano P; Alvarez R; Vesperinas A; San Millan B; Navarro C; Ravenscroft G; Illa I; Deveson I; Gallardo E, 2022, 'P.156 Novel repeat expansions in PLIN4 in two Spanish families suffering from autosomal dominant distal myopathy with unique pathological features', in Neuromuscular Disorders, Elsevier, Vol. 32, pp. s110, http://dx.doi.org/10.1016/j.nmd.2022.07.284

Working Papers

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell E; Nair SS; Zotenko E; Gould CM; Buckley M; Kaczorowski D; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2020.10.15.338855

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

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