By Dr Ira William Deveson

Journal articles

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, pp. 3934, http://dx.doi.org/10.1038/s41598-021-83642-x

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

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

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

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

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

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

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