Select Publications

Journal articles

Dey P; Mattick JS, 2021, 'High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs', Epigenetics and Chromatin, vol. 14, http://dx.doi.org/10.1186/s13072-021-00419-2

Begik O; Lucas MC; Pryszcz LP; Ramirez JM; Medina R; Milenkovic I; Cruciani S; Liu H; Vieira HGS; Sas-Chen A; Mattick JS; Schwartz S; Novoa EM, 2021, 'Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing', Nature Biotechnology, vol. 39, pp. 1278 - 1291, http://dx.doi.org/10.1038/s41587-021-00915-6

Werner A; Clark JE; Samaranayake C; Casement J; Zinad HS; Sadeq S; Al-Hashimi S; Smith M; Kotaja N; Mattick JS, 2021, 'Widespread formation of double-stranded RNAs in testis', Genome Research, vol. 31, pp. 1174 - 1186, http://dx.doi.org/10.1101/gr.265603.120

Jonkhout N; Cruciani S; Santos Vieira HG; Tran J; Liu H; Liu G; Pickford R; Kaczorowski D; Franco GR; Vauti F; Camacho N; Abedini SS; Najmabadi H; Ribas de Pouplana L; Christ D; Schonrock N; Mattick JS; Novoa EM, 2021, 'Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation', RNA Biology, vol. 18, pp. 1905 - 1919, http://dx.doi.org/10.1080/15476286.2021.1881291

Doble B; Schofield D; Evans CA; Groza T; Mattick JS; Field M; Roscioli T, 2020, 'Impacts of genomics on the health and social costs of intellectual disability', Journal of Medical Genetics, vol. 57, pp. 479 - 486, http://dx.doi.org/10.1136/jmedgenet-2019-106445

Pineda SS; Chin YKY; Undheim EAB; Senff S; Mobli M; Dauly C; Escoubas P; Nicholson GM; Kaas Q; Guo S; Herzig V; Mattick JS; King GF, 2020, 'Structural venomics reveals evolution of a complex venom by duplication and diversification of an ancient peptide-encoding gene', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, pp. 11399 - 11408, http://dx.doi.org/10.1073/pnas.1914536117

Begik O; Lucas MC; Liu H; Ramirez JM; Mattick JS; Novoa EM, 2020, 'Integrative analyses of the RNA modification machinery reveal tissue- And cancer-specific signatures', Genome Biology, vol. 21, pp. 97, http://dx.doi.org/10.1186/s13059-020-02009-z

Liu H; Begik O; Lucas MC; Ramirez JM; Mason CE; Wiener D; Schwartz S; Mattick JS; Smith MA; Novoa EM, 2019, 'Accurate detection of m6A RNA modifications in native RNA sequences', Nature Communications, vol. 10, pp. 4079, http://dx.doi.org/10.1038/s41467-019-11713-9

Habic A; Mattick JS; Calin GA; Krese R; Konc J; Kunej T, 2019, 'Genetic Variations of Ultraconserved Elements in the Human Genome', OMICS A Journal of Integrative Biology, vol. 23, pp. 549 - 559, http://dx.doi.org/10.1089/omi.2019.0156

Ke YD; Chan G; Stefanoska K; Au C; Bi M; Müller J; Przybyla M; Feiten A; Prikas E; Halliday GM; Piguet O; Kiernan MC; Kassiou M; Hodges JR; Loy CT; Mattick JS; Ittner A; Kril JJ; Sutherland GT; Ittner LM, 2019, 'CNS cell type-specific gene profiling of P301S tau transgenic mice identifies genes dysregulated by progressive tau accumulation', Journal of Biological Chemistry, vol. 294, pp. 14149 - 14162, http://dx.doi.org/10.1074/jbc.RA118.005263

Liu H; Begik O; Lucas M; Mason C; Schwartz S; Mattick J; Smith M; Novoa EM, 2019, 'Accurate detection of m6A RNA modifications in native RNA sequences', Nature Communications, vol. 10, http://dx.doi.org/10.1101/525741

Hardwick SA; Bassett SD; Kaczorowski D; Blackburn J; Barton K; Bartonicek N; Carswell SL; Tilgner HU; Loy C; Halliday G; Mercer TR; Smith MA; Mattick JS, 2019, 'Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions', Frontiers in Genetics, vol. 10, http://dx.doi.org/10.3389/fgene.2019.00309

Dong X; Liao Z; Gritsch D; Hadzhiev Y; Bai Y; Locascio JJ; Guennewig B; Liu G; Blauwendraat C; Wang T; Adler CH; Hedreen JC; Faull RLM; Frosch MP; Nelson PT; Rizzu P; Cooper AA; Heutink P; Beach TG; Mattick JS; Müller F; Scherzer CR, 2018, 'Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease', Nature Neuroscience, vol. 21, pp. 1482 - 1492, http://dx.doi.org/10.1038/s41593-018-0223-0

Mattick JS, 2018, 'The state of long non-coding RNA biology', Non-coding RNA, vol. 4, http://dx.doi.org/10.3390/ncrna4030017

Mladenova D; Barry G; Konen LM; Pineda SS; Guennewig B; Avesson L; Zinn R; Schonrock N; Bitar M; Jonkhout N; Crumlish L; Kaczorowski DC; Gong A; Pinese M; Franco GR; Walkley CR; Vissel B; Mattick JS, 2018, 'Adar3 is involved in learning and memory in mice', Frontiers in Neuroscience, vol. 12, http://dx.doi.org/10.3389/fnins.2018.00243

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, vol. 6, pp. 245 - 255.e5, http://dx.doi.org/10.1016/j.cels.2017.12.005

Mattick J, 2018, 'Four ways precision medicine is making a difference', The Conversation

Hobbs M; Ender C; Baillie GJ; Crawford J; Ru K; Taft RJ; Mattick J, 2018, 'Transcription initiation RNAs are associated with chromatin activation mark H3K4me3', BIORXIV, http://dx.doi.org/10.1101/265827

Mattick JS; Dinger M; Schonrock N; Cowley M, 2018, 'Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing', Medical Journal of Australia, vol. 209, pp. 197, http://dx.doi.org/10.5694/mja17.01176

Smith MA; Seemann SE; Quek XC; Mattick JS, 2017, 'DotAligner: Identification and clustering of RNA structure motifs', Genome Biology, vol. 18, http://dx.doi.org/10.1186/s13059-017-1371-3

Bartonicek N; Clark MB; Quek XC; Torpy JR; Pritchard AL; Maag JLV; Gloss BS; Crawford J; Taft RJ; Hayward NK; Montgomery GW; Mattick JS; Mercer TR; Dinger ME, 2017, 'Intergenic disease-associated regions are abundant in novel transcripts', Genome Biology, vol. 18, http://dx.doi.org/10.1186/s13059-017-1363-3

Doble B; Schofield DJ; Roscioli T; Mattick JS, 2017, 'Prioritising the application of genomic medicine', npj Genomic Medicine, vol. 2, http://dx.doi.org/10.1038/s41525-017-0037-0

Jonkhout N; Tran J; Smith MA; Schonrock N; Mattick JS; Novoa Pardo EM, 2017, 'The RNA modification landscape in human disease', RNA, vol. 23, pp. 1754 - 1769, http://dx.doi.org/10.1261/rna.063503.117

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

Novoa Pardo EM; Mason CE; Mattick JS, 2017, 'Charting the unknown epitranscriptome', Nature Reviews Molecular Cell Biology, vol. 18, pp. 339 - 340, http://dx.doi.org/10.1038/nrm.2017.49

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, vol. 3, http://dx.doi.org/10.1126/sciadv.1700731

Baynam G; Broley S; Bauskis A; Pachter N; McKenzie F; Townshend S; Slee J; Kiraly-Borri C; Vasudevan A; Hawkins A; Schofield L; Helmholz P; Palmer R; Kung S; Walker CE; Molster C; Lewis B; Mina K; Beilby J; Pathak G; Poulton C; Groza T; Zankl A; Roscioli T; Dinger ME; Mattick JS; Gahl W; Groft S; Tifft C; Taruscio D; Lasko P; Kosaki K; Wilhelm H; Melegh B; Carapetis J; Jana S; Chaney G; Johns A; Owen PW; Daly F; Weeramanthri T; Dawkins H; Goldblatt J, 2017, 'Initiating an undiagnosed diseases program in the Western Australian public health system', Orphanet Journal of Rare Diseases, vol. 12, http://dx.doi.org/10.1186/s13023-017-0619-z

Barry G; Briggs JA; Hwang DW; Nayler SP; Fortuna PRJ; Jonkhout N; Dachet F; Maag JLV; Mestdagh P; Singh EM; Avesson L; Kaczorowski DC; Ozturk E; Jones NC; Vetter I; Arriola-Martinez L; Hu J; Franco GR; Warn VM; Gong A; Dinger ME; Rigo F; Lipovich L; Morris MJ; O'Brien TJ; Lee DS; Loeb JA; Blackshaw S; Mattick JS; Wolvetang EJ, 2017, 'The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states', Scientific Reports, vol. 7, http://dx.doi.org/10.1038/srep40127

Robinson KM; Crabtree J; Mattick JSA; Anderson KE; Hotopp JCD, 2017, 'Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data', Microbiome, vol. 5, http://dx.doi.org/10.1186/s40168-016-0224-8

Baynam G; Bowman F; Lister K; Walker CE; Pachter N; Goldblatt J; Boycott KM; Gahl WA; Kosaki K; Adachi T; Ishii K; Mahede T; McKenzie F; Townshend S; Slee J; Kiraly-Borri C; Vasudevan A; Hawkins A; Broley S; Schofield L; Verhoef H; Groza T; Zankl A; Robinson PN; Haendel M; Brudno M; Mattick JS; Dinger ME; Roscioli T; Cowley MJ; Olry A; Hanauer M; Alkuraya FS; Taruscio D; Posada De La Paz M; Lochmüller H; Bushby K; Thompson R; Hedley V; Lasko P; Mina K; Beilby J; Tifft C; Davis M; Laing NG; Julkowska D; Le Cam Y; Terry SF; Kaufmann P; Eerola I; Norstedt I; Rath A; Suematsu M; Groft SC; Austin CP; Draghia-Akli R; Weeramanthri TS; Molster C; Dawkins HJS, 2017, 'Improved diagnosis and care for rare diseases through implementation of precision public health framework', Advances in Experimental Medicine and Biology, vol. 1031, pp. 55 - 94, http://dx.doi.org/10.1007/978-3-319-67144-4_4

Smith MA; Mattick JS, 2017, 'Structural and functional annotation of long noncoding RNAs', Methods in Molecular Biology, vol. 1526, pp. 65 - 85, http://dx.doi.org/10.1007/978-1-4939-6613-4_4

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, vol. 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, vol. 13, pp. 792 - 798, http://dx.doi.org/10.1038/nmeth.3958

Schonrock N; Jonkhout N; Mattick JS, 2016, 'Seq and you will find', Current Gene Therapy, vol. 16, pp. 220 - 229, http://dx.doi.org/10.2174/1566523216666160524144159

Bell CC; Amaral PP; Kalsbeek A; Magor GW; Gillinder KR; Tangermann P; Di Lisio L; Cheetham SW; Gruhl F; Frith J; Tallack MR; Ru KL; Crawford J; Mattick JS; Dinger ME; Perkins AC, 2016, 'The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep26657

Lu Z; Zhang QC; Lee B; Flynn RA; Smith MA; Robinson JT; Davidovich C; Gooding AR; Goodrich KJ; Mattick JS; Mesirov JP; Cech TR; Chang HY, 2016, 'RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure', Cell, vol. 165, pp. 1267 - 1279, http://dx.doi.org/10.1016/j.cell.2016.04.028

Bussotti G; Leonardi T; Clark MB; Mercer TR; Crawford J; Malquori L; Notredame C; Dinger ME; Mattick JS; Enright AJ, 2016, 'Improved definition of the mouse transcriptome via targeted RNA sequencing', Genome Research, vol. 26, pp. 705 - 716, http://dx.doi.org/10.1101/gr.199760.115

Doble B; Schofield DJ; Roscioli T; Mattick JS, 2016, 'The promise of personalised medicine', The Lancet, vol. 387, pp. 433 - 434, http://dx.doi.org/10.1016/S0140-6736(16)00176-8

Zhao W; Mazar J; Lee B; Sawada J; Li JL; Shelley J; Govindarajan S; Towler D; Mattick JS; Komatsu M; Dinger ME; Perera RJ, 2016, 'The Long Noncoding RNA SPRIGHTLY Regulates Cell Proliferation in Primary Human Melanocytes', Journal of Investigative Dermatology, vol. 136, pp. 819 - 828, http://dx.doi.org/10.1016/j.jid.2016.01.018

Spadaro PA; Flavell CR; Widagdo J; Ratnu VS; Troup M; Ragan C; Mattick JS; Bredy TW, 2015, 'Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated with Anxiety-like Behavior in Mice', Biological Psychiatry, vol. 78, pp. 848 - 859, http://dx.doi.org/10.1016/j.biopsych.2015.02.004

Briggs JA; Wolvetang EJ; Mattick JS; Rinn JL; Barry G, 2015, 'Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution', Neuron, vol. 88, pp. 861 - 877, http://dx.doi.org/10.1016/j.neuron.2015.09.045

Ferracin M; Gautheret D; Hubé F; Mani SA; Mattick JS; Ørom UA; Santulli G; Slotkin RK; Szweykowska-Kulinska Z; Taube JH; Vazquez F; Yang JH, 2015, 'The non-coding RNA journal club: Highlights on recent papers', Non-coding RNA, vol. 1, pp. 87 - 93, http://dx.doi.org/10.3390/ncrna1010087

Sapkota S; Brien J-AE; Greenfield JR; Aslani P, 2015, 'A Systematic Review of Interventions Addressing Adherence to Anti-Diabetic Medications in Patients with Type 2 Diabetes—Components of Interventions', PLOS ONE, vol. 10, pp. e0128581 - e0128581, http://dx.doi.org/10.1371/journal.pone.0128581

Werner A; Piatek MJ; Mattick JS, 2015, 'Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms', Annals of the New York Academy of Sciences, vol. 1341, pp. 156 - 163, http://dx.doi.org/10.1111/nyas.12608

Clark MB; Mercer TR; Bussotti G; Leonardi T; Haynes KR; Crawford J; Brunck ME; Cao KAL; Thomas GP; Chen WY; Taft RJ; Nielsen LK; Enright AJ; Mattick JS; Dinger ME, 2015, 'Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing', Nature Methods, vol. 12, pp. 339 - 342, http://dx.doi.org/10.1038/nmeth.3321

Londina E; Lohera P; Telonis AG; Quann K; Clark P; Jinga Y; Hatzimichael E; Kirino Y; Honda S; Lally M; Ramratnam B; Comstock CES; Knudsen KE; Gomella L; Spaeth GL; Hark L; Katz LJ; Witkiewicz A; Rostami A; Jimenez SA; Hollingsworth MA; Yeh JJ; Shaw CA; McKenzie SE; Bray P; Nelson PT; Zupo S; Van Roosbroeck K; Keating MJ; Calin GA; Yeo C; Jimbo M; Cozzitorto J; Brody JR; Delgrosso K; Mattick JS; Fortina P; Rigoutsos I, 2015, 'Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- And tissue-specific microRNAs', Proceedings of the National Academy of Sciences of the United States of America, vol. 112, pp. E1106 - E1115, http://dx.doi.org/10.1073/pnas.1420955112

Roadmap Epigenomics Consortium ; Kundaje A; Meuleman W; Ernst J; Bilenky M; Yen A; Heravi-Moussavi A; Kheradpour P; Zhang Z; Wang J; Ziller MJ; Amin V; Whitaker JW; Schultz MD; Ward LD; Sarkar A; Quon G; Sandstrom RS; Eaton ML; Wu YC; Pfenning AR; Wang X; Claussnitzer M; Liu Y; Coarfa C; Harris RA; Shoresh N; Epstein CB; Gjoneska E; Leung D; Xie W; Hawkins RD; Lister R; Hong C; Gascard P; Mungall AJ; Moore R; Chuah E; Tam A; Canfield TK; Hansen RS; Kaul R; Sabo PJ; Bansal MS; Carles A; Dixon JR; Farh KH; Feizi S; Karlic R; Kim AR; Kulkarni A; Li D; Lowdon R; Elliott G; Mercer TR; Neph SJ; Onuchic V; Polak P; Rajagopal N; Ray P; Sallari RC; Siebenthall KT; Sinnott-Armstrong NA; Stevens M; Thurman RE; Wu J; Zhang B; Zhou X; Beaudet AE; Boyer LA; De Jager PL; Farnham PJ; Fisher SJ; Haussler D; Jones SJM; Li W; Marra MA; McManus MT; Sunyaev S; Thomson JA; Tlsty TD; Tsai LH; Wang W; Waterland RA; Zhang MQ; Chadwick LH; Bernstein BE; Costello JF; Ecker JR; Hirst M; Meissner A; Milosavljevic A; Ren B; Stamatoyannopoulos JA; Wang T; Kellis M, 2015, 'Integrative analysis of 111 reference human epigenomes', Nature, vol. 518, pp. 317 - 329, http://dx.doi.org/10.1038/nature14248

Mercer TR; Clark MB; Andersen SB; Brunck ME; Haerty W; Crawford J; Taft RJ; Nielsen LK; Dinger ME; Mattick JS, 2015, 'Genome-wide discovery of human splicing branchpoints', Genome Research, vol. 25, pp. 290 - 303, http://dx.doi.org/10.1101/gr.182899.114

Mattick JS; Rinn JL, 2015, 'Discovery and annotation of long noncoding RNAs', Nature Structural and Molecular Biology, vol. 22, pp. 5 - 7, http://dx.doi.org/10.1038/nsmb.2942

Liu PY; Erriquez D; Marshall GM; Tee AE; Polly P; Wong M; Liu B; Bell JL; Zhang XD; Milazzo G; Cheung BB; Fox A; Swarbrick A; Hüttelmaier S; Kavallaris M; Perini G; Mattick JS; Dinger ME; Liu T, 2015, 'Erratum: Effects of a novel long noncoding RNA, lncUSMycN, on N-Myc expression and neuroblastoma progression (Journal of the National Cancer Institute (2014) 106:7 (dju113) DOI: 10.1093/jnci/dju113)', Journal of the National Cancer Institute, vol. 107, http://dx.doi.org/10.1093/jnci/dju359


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