By Dr Ira William Deveson

Journal articles

Whiteley SL; Holleley CE; Wagner S; Blackburn J; Deveson IW; Marshall Graves JA; Georges A, 2021, 'Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination', PLoS Genetics, 17, http://dx.doi.org/10.1371/journal.pgen.1009465

O'Toole Á; Kraemer MUG; Hill V; Pybus OG; Watts A; Bogoch II; Khan K; Messina JP; Tegally H; Lessells RR; Giandhari J; Pillay S; Tumedi KA; Nyepetsi G; Kebabonye M; Matsheka M; Mine M; Tokajian S; Hassan H; Salloum T; Merhi G; Koweyes J; Geoghegan JL; de Ligt J; Ren X; Storey M; Freed NE; Pattabiraman C; Prasad P; Desai AS; Vasanthapuram R; Schulz TF; Steinbrück L; Stadler T; Parisi A; Bianco A; García de Viedma D; Buenestado-Serrano S; Borges V; Isidro J; Duarte S; Gomes JP; Zuckerman NS; Mandelboim M; Mor O; Seemann T; Arnott A; Draper J; Gall M; Rawlinson W; Deveson I; Schlebusch S; McMahon J; Leong L; Lim CK; Chironna M; Loconsole D; Bal A; Josset L; Holmes E; St. George K; Lasek-Nesselquist E; Sikkema RS; Oude Munnink B; Koopmans M; Brytting M; Sudha rani V; Pavani S; Smura T; Heim A; Kurkela S; Umair M; Salman M; Bartolini B; Rueca M; Drosten C; Wolff T; Silander O; Eggink D; Reusken C; Vennema H; Park A; Carrington C; Sahadeo N; Carr M; Gonzalez G; de Oliveira T; Faria N; Rambaut A, 2021, 'Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2', Wellcome Open Research, 6, http://dx.doi.org/10.12688/wellcomeopenres.16661.1

Ferguson J; Gamaarachchi H; Nguyen T; Gollon A; Tong S; Aquilina-Reid C; Bowen-James R; Deveson I, 2021, '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

Foster CSP; Stelzer-Braid S; Deveson I; Bull R; Yeang M; Phan-Au J; Silva MR; van Hal S; Rockett R; Sintchenko V; Kim KW; Rawlinson W, 2021, '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

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, 2021, 'SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis', , http://dx.doi.org/10.1101/2021.06.29.450255

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, 2021, 'SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis', , http://dx.doi.org/10.21203/rs.3.rs-668517/v1

Whiteley S; Holleley C; Wagner S; Blackburn J; Deveson I; Graves JM; Georges A, 2021, 'Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination', , http://dx.doi.org/10.1101/2021.02.03.429474

Reis ALM; Deveson IW; Wong T; Madala BS; Barker C; Blackburn J; Marcellin E; Mercer TR, 2020, 'A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-17445-5

Bull RA; Adikari TN; Ferguson JM; Hammond JM; Stevanovski I; Beukers AG; Naing Z; Yeang M; Verich A; Gamaarachchi H; Kim KW; Luciani F; Stelzer-Braid S; Eden JS; Rawlinson WD; van Hal SJ; Deveson IW, 2020, 'Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-20075-6

Heyer EE; Deveson IW; Wooi D; Selinger CI; Lyons RJ; Hayes VM; O’Toole SA; Ballinger ML; Gill D; Thomas DM; Mercer TR; Blackburn J; O'Toole S, 2020, 'Author Correction: Diagnosis of fusion genes using targeted RNA sequencing (Nature Communications, (2019), 10, 1, (1388), 10.1038/s41467-019-09374-9)', Nature Communications, 11, pp. 1810, http://dx.doi.org/10.1038/s41467-020-15697-9

Samarakoon H; Punchihewa S; Senanayake A; Hammond JM; Stevanovski I; Ferguson JM; Ragel R; Gamaarachchi H; Deveson IW, 2020, 'Genopo: a nanopore sequencing analysis toolkit for portable Android devices', Communications Biology, 3, http://dx.doi.org/10.1038/s42003-020-01270-z

Kim KW; Deveson I; Pang CN; Yeang M; Naing Z; Adikari T; Hammond J; Stevanovski I; Beukers A; Verich A; Yin S; McFarlane D; Wilkins M; Stelzer-Braid S; Bull R; Craig M; Hal SV; Rawlinson W, 2020, '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

Deveson IW; Madala BS; Blackburn J; Barker C; Wong T; Barton KM; Smith MA; Watkins DN; Mercer TR, 2019, 'Chiral DNA sequences as commutable controls for clinical genomics', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-09272-0

Heyer EE; Deveson IW; Wooi D; Selinger CI; Lyons RJ; Hayes VM; O’Toole SA; Ballinger ML; Gill D; Thomas DM; Mercer TR; Blackburn J; O'Toole S, 2019, 'Diagnosis of fusion genes using targeted RNA sequencing', Nature Communications, 10, pp. 1388, http://dx.doi.org/10.1038/s41467-019-09374-9

Blackburn J; Wong T; Madala BS; Barker C; Hardwick SA; Reis ALM; Deveson IW; Mercer TR, 2019, 'Use of synthetic DNA spike-in controls (sequins) for human genome sequencing', Nature Protocols, 14, pp. 2119 - 2151, http://dx.doi.org/10.1038/s41596-019-0175-1

Hardwick SA; Chen WY; Wong T; Kanakamedala BS; Deveson IW; Ongley SE; Santini NS; Marcellin E; Smith MA; Nielsen LK; Lovelock CE; Neilan BA; Mercer TR, 2018, 'Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis', Nature Communications, 9, http://dx.doi.org/10.1038/s41467-018-05555-0

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', BIORXIV, http://dx.doi.org/10.1101/404285

Deveson IW; Brunck ME; Blackburn J; Tseng E; Hon T; Clark TA; Clark MB; Crawford J; Dinger ME; Nielsen LK; Mattick JS; Mercer TR, 2018, 'Universal Alternative Splicing of Noncoding Exons', Cell Systems, 6, pp. 245 - 255.e5, http://dx.doi.org/10.1016/j.cels.2017.12.005

Hardwick SA; Deveson IW; Mercer TR, 2017, 'Reference standards for next-generation sequencing', Nature Reviews Genetics, 18, pp. 473 - 484, http://dx.doi.org/10.1038/nrg.2017.44

Zheng Z; Reichel M; Deveson I; Wong G; Li J; Millar AA, 2017, 'Target RNA secondary structure is a major determinant of miR159 efficacy', Plant Physiology, 174, pp. 1764 - 1778, http://dx.doi.org/10.1104/pp.16.01898

Deveson IW; Hardwick SA; Mercer TR; Mattick JS, 2017, 'The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome', Trends in Genetics, 33, pp. 464 - 478, http://dx.doi.org/10.1016/j.tig.2017.04.004

Wong T; Deveson IW; Hardwick SA; Mercer TR, 2017, 'ANAQUIN: A software toolkit for the analysis of spike-in controls for next generation sequencing', Bioinformatics, 33, pp. 1723 - 1724, http://dx.doi.org/10.1093/bioinformatics/btx038

Deveson IW; Holleley CE; Blackburn J; Marshall Graves JA; Mattick JS; Waters PD; Georges A, 2017, 'Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination', Science Advances, 3, pp. e1700731, http://dx.doi.org/10.1126/sciadv.1700731

Deveson IW; Chen WY; Wong T; Hardwick SA; Andersen SB; Nielsen LK; Mattick JS; Mercer TR, 2016, 'Representing genetic variation with synthetic DNA standards', Nature Methods, 13, pp. 784 - 791, http://dx.doi.org/10.1038/nmeth.3957

Hardwick SA; Chen WY; Wong T; Deveson IW; Blackburn J; Andersen SB; Nielsen LK; Mattick JS; Mercer TR, 2016, 'Spliced synthetic genes as internal controls in RNA sequencing experiments', Nature Methods, 13, pp. 792 - 798, http://dx.doi.org/10.1038/nmeth.3958

Deveson I; Li J; Millar AA, 2013, 'MicroRNAs with analogous target complementarities perform with highly variable efficacies in Arabidopsis', FEBS Letters, 587, pp. 3703 - 3708, http://dx.doi.org/10.1016/j.febslet.2013.09.037

Deveson I; Li J; Millar AA, 2013, 'Expression of human ARGONAUTE 2 inhibits endogenous microRNA activity in Arabidopsis', Frontiers in Plant Science, 4, http://dx.doi.org/10.3389/fpls.2013.00096

Conference Papers

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

Olive M; Stevanovski I; Gonzalez Quereda L; 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, 'Novel repeat expansions in PLIN4 in two Spanish families suffering from autosomal dominant distal myopathy with unique pathological features', in NEUROMUSCULAR DISORDERS, PERGAMON-ELSEVIER SCIENCE LTD, Vol. 32, pp. S110 - S110, http://dx.doi.org/10.1016/j.nmd.2022.07.284

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

Working Papers

Du Q; Smith G; Luu PL; Ferguson J; Armstrong N; Caldon E; Campbell E; Nair S; Zotenko E; Gould C; Buckley M; Kaczorowski D; Barton K; Deveson I; Smith M; Powell J; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark S, 2020, DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity, http://dx.doi.org10.1101/2020.10.15.338855

Preprints

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

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 inMMEcauses 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

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