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Dr Ira Deveson

Dr Ira Deveson

Conjoint Lecturer

Doctor of Philosophy (biological sciences). Garvan / UNSW (2014-2017).

Bachelor of Philosophy (science), first class honours. Australian National University (2009-12).

Medicine & Health
School of Clinical Medicine

Dr Ira Deveson graduated with a Bachelor of Philosophy from the Australian National University in 2012. He completed a PhD at the Garvan Institute from 2014-2017, supervised by Prof John Mattick and Dr Tim Mercer.  Dr Deveson's PhD was focused on genome/transcriptome research and bioinfomatics, and earned him recognition with the JD Catcheside prize from the Genomics Society of Australasia.

Dr Deveson was awarded an Early Career Fellowship from the Cancer Institute NSW (2018) and a prestigious Investigator Grant (EL2) from the NHMRC and Medical Research Futures Fund (2020). After a post-doc stint under Dr Tim Mercer, he was appointed as Head of the Genomic Technologies Group within the Kinghorn Centre for Clinical Genomics in 2020. Under Dr Deveson's leadership, the Genome Technologies Group is testing and developing cutting-edge molecular and computational tools for research and clinical genomics.
Phone
9355 5883
E-mail
i.deveson@garvan.org.au
Location
Garvan Institute, 384 Victoria Street, Darlinghurst NSW 2010
  • Journal articles | 2023
    Barton K; Ferguson JM; Deveson IW; Falcinelli SD; James KS; Kirchherr J; Ramirez C; Gay CL; Hammond JM; Bevear B; Carswell SL; Margolis DM; Smith MA; Adimora AA; Archin NM, 2023, 'HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women', Journal of Virology, 97, http://dx.doi.org/10.1128/jvi.00705-23
    Journal articles | 2023
    Dominik N; Magri S; Currò R; Abati E; Facchini S; Corbetta M; MacPherson H; Di Bella D; Sarto E; Stevanovski I; Chintalaphani SR; Akcimen F; Manini A; Vegezzi E; Quartesan I; Montgomery KA; Pirota V; Crespan E; Perini C; Grupelli GP; Tomaselli PJ; Marques W; Ambrose JC; Arumugam P; Baple EL; Bleda M; Boardman-Pretty F; Boissiere JM; Boustred CR; Brittain H; Caulfield MJ; Chan GC; Craig CEH; Daugherty LC; De Burca A; Devereau A; Elgar G; Foulger RE; Fowler T; Furió-Tarí P; Gustavsson E; Hackett JM; Halai D; Hamblin A; Henderson S; Holman JE; Hubbard TJP; Ibáñez K; Jackson R; Jones LJ; Kasperaviciute D; Kayikci M; Lahnstein L; Lawson K; Leigh SEA; Leong IUS; Lopez FJ; Maleady-Crowe F; Mason J; McDonagh EM; Moutsianas L; Mueller M; Murugaesu N; Need AC; Odhams CA; Patch C; Perez-Gil D; Polychronopoulos D; Pullinger J; Rahim T; Rendon A; Riesgo-Ferreiro P; Rogers T; Ryten M; Rugginini B; Savage K; Sawant K; Scott RH; Siddiq A; Sieghart A; Smedley D; Smith KR; Sosinsky A; Spooner W; Stevens HE; Stuckey A; Sultana R; Thomas ERA; Thompson SR; Tregidgo C; Tucci A; Walsh E; Watters SA; Welland MJ; Williams E; Witkowska K; Wood SM; Zarowiecki M; Shaw J; Polke J, 2023, 'Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis', Brain, 146, pp. 5060 - 5069, http://dx.doi.org/10.1093/brain/awad240
    Journal articles | 2023
    Folland C; Ganesh V; Weisburd B; McLean C; Kornberg AJ; O'Donnell-Luria A; Rehm HL; Stevanovski I; Chintalaphani SR; Kennedy P; Deveson IW; Ravenscroft G, 2023, 'Transcriptome and Genome Analysis Uncovers a DMD Structural Variant: A Case Report.', Neurol Genet, 9, pp. e200064, http://dx.doi.org/10.1212/NXG.0000000000200064
    Journal articles | 2023
    Hort Y; Sullivan P; Wedd L; Fowles L; Stevanovski I; Deveson I; Simons C; Mallett A; Patel C; Furlong T; Cowley MJ; Shine J; Mallawaarachchi A, 2023, 'Atypical splicing variants in PKD1 explain most undiagnosed typical familial ADPKD', npj Genomic Medicine, 8, http://dx.doi.org/10.1038/s41525-023-00362-z
    Journal articles | 2023
    Louie RHY; Cai C; Samir J; Singh M; Deveson IW; Ferguson JM; Amos TG; McGuire HM; Gowrishankar K; Adikari T; Balderas R; Bonomi M; Ruella M; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2023, 'CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies', Nature Communications, 14, http://dx.doi.org/10.1038/s41467-023-43656-7
    Journal articles | 2023
    Luciani F; Louie RY; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire H; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottileb D; Blyth E; Micklethwaite K, 2023, 'CAR +and CAR −T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion', The Journal of Immunology, 210, pp. 159.15 - 159.15, http://dx.doi.org/10.4049/jimmunol.210.supp.159.15
    Journal articles | 2023
    Ludington AJ; Hammond JM; Breen J; Deveson IW; Sanders KL, 2023, 'New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)', BMC Biology, 21, http://dx.doi.org/10.1186/s12915-023-01772-2
    Journal articles | 2023
    Reis ALM; Rapadas M; Hammond JM; Gamaarachchi H; Stevanovski I; Ayuputeri Kumaheri M; Chintalaphani SR; Dissanayake DSB; Siggs OM; Hewitt AW; Llamas B; Brown A; Baynam G; Mann GJ; McMorran BJ; Easteal S; Hermes A; Jenkins MR; Pearson G; Roe Y; Mohamed J; Murray B; Ormond-Parker L; Kneipp E; Nugent K; Mann G; Patel HR; Deveson IW, 2023, 'The landscape of genomic structural variation in Indigenous Australians', Nature, http://dx.doi.org/10.1038/s41586-023-06842-7
    Journal articles | 2023
    Samarakoon H; Ferguson JM; Gamaarachchi H; Deveson IW, 2023, 'Accelerated nanopore basecalling with SLOW5 data format', Bioinformatics, 39, http://dx.doi.org/10.1093/bioinformatics/btad352
    Journal articles | 2023
    Samarakoon H; Ferguson JM; Jenner SP; Amos TG; Parameswaran S; Gamaarachchi H; Deveson IW, 2023, 'Flexible and efficient handling of nanopore sequencing signal data with slow5tools', Genome Biology, 24, http://dx.doi.org/10.1186/s13059-023-02910-3
    Journal articles | 2023
    Scriba CK; Stevanovski I; Chintalaphani SR; Gamaarachchi H; Ghaoui R; Ghia D; Henderson RD; Jordan N; Winkel A; Lamont PJ; Rodrigues MJ; Roxburgh RH; Weisburd B; Laing NG; Deveson IW; Davis MR; Ravenscroft G, 2023, 'RFC1 in an Australasian neurological disease cohort: Extending the genetic heterogeneity and implications for diagnostics', Brain Communications, 5, pp. fcad208, http://dx.doi.org/10.1093/braincomms/fcad208
    Journal articles | 2023
    Wagner S; Whiteley SL; Castelli M; Patel HR; Deveson IW; Blackburn J; Holleley CE; Marshall Graves JA; Georges A, 2023, 'Gene expression of male pathway genes sox9 and amh during early sex differentiation in a reptile departs from the classical amniote model', BMC Genomics, 24, http://dx.doi.org/10.1186/s12864-023-09334-0
    Journal articles | 2023
    Williams LJ; Qiu J; Ong TL; Deveson IW; Stevanovski I; Chintalaphani SR; Fellner A; Varikatt W; Morales-Briceno H; Tchan M; Kumar KR; Fung VSC, 2023, 'NOTCH2NLC GGC Repeat Expansion Presenting as Adult-Onset Cervical Dystonia', Movement Disorders Clinical Practice, 10, pp. 704 - 706, http://dx.doi.org/10.1002/mdc3.13677
    Journal articles | 2023
    Williams TC; Kroukamp H; Xu X; Wightman ELI; Llorente B; Borneman AR; Carpenter AC; Van Wyk N; Meier F; Collier TRV; 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, 2023, 'Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects', Cell Genomics, 3, http://dx.doi.org/10.1016/j.xgen.2023.100379
    Journal articles | 2022
    Bartonicek N; Rouet R; Warren J; Loetsch C; Rodriguez GS; Walters S; Lin F; Zahra D; Blackburn J; Hammond JM; Reis ALM; Deveson IW; Zammit N; Zeraati M; Grey S; Christ D; Mattick JS; Chtanova T; Brink R; Dinger ME; Weatheritt RJ; Sprent J; King C, 2022, 'The retroelement Lx9 puts a brake on the immune response to virus infection', Nature, 608, pp. 757 - 765, http://dx.doi.org/10.1038/s41586-022-05054-9
    Journal articles | 2022
    Ferguson JM; Gamaarachchi H; Nguyen T; Gollon A; Tong S; Aquilina-Reid C; Bowen-James R; Deveson IW, 2022, 'InterARTIC: An interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses', Bioinformatics, 38, pp. 1443 - 1446, http://dx.doi.org/10.1093/bioinformatics/btab846
    Journal articles | 2022
    Foster CSP; Stelzer-Braid S; Deveson IW; Bull RA; Yeang M; Au JP; Ruiz Silva M; van Hal SJ; Rockett RJ; Sintchenko V; Kim KW; Rawlinson WD, 2022, 'Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia', Viruses, 14, http://dx.doi.org/10.3390/v14020185
    Journal articles | 2022
    Gamaarachchi H; Samarakoon H; Jenner SP; Ferguson JM; Amos TG; Hammond JM; Saadat H; Smith MA; Parameswaran S; Deveson IW, 2022, 'Fast nanopore sequencing data analysis with SLOW5', Nature Biotechnology, 40, pp. 1026 - 1029, http://dx.doi.org/10.1038/s41587-021-01147-4
    Journal articles | 2022
    Gong B; Deveson IW; Mercer T; Johann DJ; Jones W; Tong W; Xu J, 2022, 'Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity', Scientific Data, 9, http://dx.doi.org/10.1038/s41597-022-01276-8
    Journal articles | 2022
    Grosz BR; Stevanovski I; Negri S; Ellis M; Barnes S; Reddel S; Vucic S; Nicholson GA; Cortese A; Kumar KR; Deveson IW; Kennerson ML, 2022, 'Long read sequencing overcomes challenges in the diagnosis of SORD neuropathy', Journal of the Peripheral Nervous System, 27, pp. 120 - 126, http://dx.doi.org/10.1111/jns.12485
    Journal articles | 2022
    Gunter HM; Youlten SE; Madala BS; Reis ALM; Stevanovski I; Wong T; Kummerfield SK; Deveson IW; Santini NS; Marcellin E; Mercer TR, 2022, 'Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-34028-8
    Journal articles | 2022
    Kim KW; Wang X; Adhikari A; Yeang M; Jenkins F; Naing Z; Walker GJ; Foster CSP; Stelzer-Braid S; Deveson I; Craig ME; Tedla N; Bull RA; Martinello M; Pinto AN; Chan R; Turville S; Rawlinson WD; van Hal S, 2022, 'Persistent high-level shedding of cultivable SARS-CoV-2 Delta virus 33 days after onset of COVID-19 in a hospitalized patient with pneumonia', Journal of Medical Virology, 94, pp. 4043 - 4046, http://dx.doi.org/10.1002/jmv.27832
    Journal articles | 2022
    Reis ALM; Deveson IW; Madala BS; Wong T; Barker C; Xu J; Lennon N; Tong W; Mercer TR, 2022, 'Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome', Genome Biology, 23, http://dx.doi.org/10.1186/s13059-021-02579-6
    Journal articles | 2022
    Reis ALM; Hammond JM; Stevanovski I; Arnold JC; McGregor IS; Deveson IW; Gururajan A, 2022, 'Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition', iScience, 25, http://dx.doi.org/10.1016/j.isci.2022.104861
    Journal articles | 2022
    Roca-Rada X; Tereso S; Rohrlach AB; Brito A; Williams MP; Umbelino C; Curate F; Deveson IW; Souilmi Y; Amorim A; Carvalho PC; Llamas B; Teixeira JC, 2022, 'A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics', The Lancet, 400, pp. 691 - 692, http://dx.doi.org/10.1016/S0140-6736(22)01476-3
    Journal articles | 2022
    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, 2022, 'Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abm5386
    Journal articles | 2022
    Whiteley SL; Wagner S; Holleley CE; Deveson IW; Marshall Graves JA; Georges A, 2022, 'Truncated jarid2 and kdm6b transcripts are associated with temperature-induced sex reversal during development in a dragon lizard', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abk0275
    Journal articles | 2022
    Zhang X; Wagner S; Holleley CE; Deakin JE; Matsubara K; Deveson IW; O’Meally D; Patel HR; Ezaz T; Li Z; Wang C; Edwards M; Marshall Graves JA; Georges A, 2022, 'Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation', Proceedings of the National Academy of Sciences of the United States of America, 119, http://dx.doi.org/10.1073/pnas.2116475119
    Journal articles | 2022
    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', NEUROMUSCULAR DISORDERS, vol. 32, pp. S110 - S110, http://dx.doi.org/10.1016/j.nmd.2022.07.284
    Journal articles | 2021
    Chintalaphani SR; Pineda SS; Deveson IW; Kumar KR, 2021, 'An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics', Acta Neuropathologica Communications, 9, http://dx.doi.org/10.1186/s40478-021-01201-x
    Journal articles | 2021
    Deveson IW; Gong B; Lai K; LoCoco JS; Richmond TA; Schageman J; Zhang Z; Novoradovskaya N; Willey JC; Jones W; Kusko R; Chen G; Madala BS; Blackburn J; Stevanovski I; Bhandari A; Close D; Conroy J; Hubank M; Marella N; Mieczkowski PA; Qiu F; Sebra R; Stetson D; Sun L; Szankasi P; Tan H; Tang LY; Arib H; Best H; Burgher B; Bushel PR; Casey F; Cawley S; Chang CJ; Choi J; Dinis J; Duncan D; Eterovic AK; Feng L; Ghosal A; Giorda K; Glenn S; Happe S; Haseley N; Horvath K; Hung LY; Jarosz M; Kushwaha G; Li D; Li QZ; Li Z; Liu LC; Liu Z; Ma C; Mason CE; Megherbi DB; Morrison T; Pabón-Peña C; Pirooznia M; Proszek PZ; Raymond A; Rindler P; Ringler R; Scherer A; Shaknovich R; Shi T; Smith M; Song P; Strahl M; Thodima VJ; Tom N; Verma S; Wang J; Wu L; Xiao W; Xu C; Yang M; Zhang G; Zhang S; Zhang Y; Shi L; Tong W; Johann DJ; Mercer TR; Xu J, 2021, 'Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology', Nature Biotechnology, 39, pp. 1115 - 1128, http://dx.doi.org/10.1038/s41587-021-00857-z
    Journal articles | 2021
    Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell EM; Nair SS; Zotenko E; Gould CM; Buckley M; Chia KM; Portman N; Lim E; Kaczorowski D; Chan CL; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, 2021, 'DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity', Cell Reports, 36, http://dx.doi.org/10.1016/j.celrep.2021.109722
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    Gong B; Li D; Kusko R; Novoradovskaya N; Zhang Y; Wang S; Pabón-Peña C; Zhang Z; Lai K; Cai W; LoCoco JS; Lader E; Richmond TA; Mittal VK; Liu LC; Johann DJ; Willey JC; Bushel PR; Yu Y; Xu C; Chen G; Burgess D; Cawley S; Giorda K; Haseley N; Qiu F; Wilkins K; Arib H; Attwooll C; Babson K; Bao L; Bao W; Lucas AB; Best H; Bhandari A; Bisgin H; Blackburn J; Blomquist TM; Boardman L; Burgher B; Butler DJ; Chang CJ; Chaubey A; Chen T; Chierici M; Chin CR; Close D; Conroy J; Coleman JC; Craig DJ; Crawford E; del Pozo A; Deveson IW; Duncan D; Eterovic AK; Fan X; Foox J; Furlanello C; Ghosal A; Glenn S; Guan M; Haag C; Hang X; Happe S; Hennigan B; Hipp J; Hong H; Horvath K; Hu J; Hung LY; Jarosz M; Kerkhof J; Kipp B; Kreil DP; Łabaj P; Lapunzina P; Li P; Li QZ; Li W; Li Z; Liang Y; Liu S; Liu Z; Ma C; Marella N; Martín-Arenas R; Megherbi DB; Meng Q; Mieczkowski PA; Morrison T; Muzny D; Ning B; Parsons BL; Paweletz CP; Pirooznia M; Qu W; Raymond A; Rindler P; Ringler R; Sadikovic B, 2021, 'Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions', Genome Biology, 22, http://dx.doi.org/10.1186/s13059-021-02315-0
    Journal articles | 2021
    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; van Hal SJ; Rawlinson WD, 2021, 'Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing', Scientific Reports, 11, http://dx.doi.org/10.1038/s41598-021-83642-x
    Journal articles | 2021
    Madala BS; Reis ALM; Deveson IW; Rawlinson W; Mercer TR, 2021, 'Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests', Scientific Reports, 11, http://dx.doi.org/10.1038/s41598-021-81760-0
    Journal articles | 2021
    O'Toole Á; 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; Kraemer MUG, 2021, 'Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch', Wellcome Open Research, 6, pp. 121 - 121, http://dx.doi.org/10.12688/wellcomeopenres.16661.2
    Journal articles | 2021
    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
    Journal articles | 2021
    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, 2021, 'No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing', Cell Reports, 36, http://dx.doi.org/10.1016/j.celrep.2021.109530
    Journal articles | 2021
    Van Thillo Q; De Bie J; Seneviratne JA; Demeyer S; Omari S; Balachandran A; Zhai V; Tam WL; Sweron B; Geerdens E; Gielen O; Provost S; Segers H; Boeckx N; Marshall GM; Cheung BB; Isobe K; Kato I; Takita J; Amos TG; Deveson IW; McCalmont H; Lock RB; Oxley EP; Garwood MM; Dickins RA; Uyttebroeck A; Carter DR; Cools J; de Bock CE, 2021, 'Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia', Nature Communications, 12, http://dx.doi.org/10.1038/s41467-021-24442-9
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    Willey JC; Morrison TB; 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 QZ; Johann DJ; Deveson IW; Mercer TR; Wu L; Xu J, 2021, 'Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA', Cell Reports Methods, 1, http://dx.doi.org/10.1016/j.crmeth.2021.100106
    Journal articles | 2020
    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
    Journal articles | 2020
    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.org/10.1101/2020.10.15.338855
    Journal articles | 2020
    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, 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, http://dx.doi.org/10.1038/s41467-020-15697-9
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2019
    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
    Journal articles | 2019
    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
    Journal articles | 2019
    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, 2019, 'Diagnosis of fusion genes using targeted RNA sequencing', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-09374-9
    Journal articles | 2018
    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
    Journal articles | 2018
    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
    Journal articles | 2018
    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
    Journal articles | 2017
    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
    Journal articles | 2017
    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, http://dx.doi.org/10.1126/sciadv.1700731
    Journal articles | 2017
    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
    Journal articles | 2017
    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
    Journal articles | 2017
    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
    Journal articles | 2016
    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
    Journal articles | 2016
    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
    Journal articles | 2013
    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
    Journal articles | 2013
    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
  • Preprints | 2023
    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
    Preprints | 2023
    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
    Preprints | 2023
    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
    Preprints | 2023
    Hanrahan BJ; Chang JK; Lister NC; Dissanayake DSB; Hammond JM; Reis ALM; Deveson IW; Ruiz-Herrera A; Patel HR; Marshall Graves JA; Georges A; Waters PD, 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
    Preprints | 2023
    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
    Preprints | 2023
    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
    Preprints | 2023
    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
    Preprints | 2023
    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
    Conference Abstracts | 2022
    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
    Preprints | 2022
    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
    Preprints | 2022
    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
    Conference Abstracts | 2022
    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
    Preprints | 2022
    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
    Preprints | 2022
    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
    Conference Papers | 2021
    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
    Preprints | 2021
    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
    Preprints | 2021
    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
    Preprints | 2021
    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
    Preprints | 2021
    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
    Preprints | 2021
    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
    Preprints | 2020
    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
    Preprints | 2020
    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
    Preprints | 2017
    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
    Preprints |
    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

MRFF Investigator Grant – Emerging Leadership Level 2 (2020-2025).

Developing synthetic DNA reference standards (sequins) to ensure accuracy in emerging genomic technologies.

Cancer Institute NSW Early Career Fellowship (2018-2020).

Representing the cancer genome with synthetic spike-in controls.

UNSW-USA Networks of Excellence Mobility Grant (2019).

Interrogating the human transcriptome with high-throughput CRIPSR knockout screens.

Garvan Rising Star Award (2018).

DG Catcheside Prize, Genetics Society of Australasia (2017).

Stuart Furler Travel Award, Garvan Institute (2016).

Graduate Research Excellence Scholarship, UNSW (2014-2017).

3 Minute Thesis winner, Garvan Institute (2014).

University Medal for Biology, Australian National University (2012).

Technology development for research and clinical genomics

Developing synthetic controls for genomics

Viral / pathogen genomics in the age of coronavirus

Gene regulation and alternative splicing at single-cell resolution

Bioinformatics and computational genomics