By Professor John Stanley Mattick

Journal articles

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, 12, pp. 83, 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, 7, pp. 40127, 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, 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, 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', , 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, 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

Schonrock N; Jonkhout N; Mattick JS, 2016, 'Seq and you will find', Current Gene Therapy, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 107, http://dx.doi.org/10.1093/jnci/dju359

Cossetti C; Iraci N; Mercer TR; Leonardi T; Alpi E; Drago D; Alfaro-Cervello C; Saini HK; Davis MP; Schaeffer J; Vega B; Stefanini M; Zhao CJ; Muller W; Garcia-Verdugo JM; Mathivanan S; Bachi A; Enright AJ; Mattick JS; Pluchino S, 2014, 'Extracellular Vesicles from Neural Stem Cells Transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells', Molecular Cell, 56, pp. 609, http://dx.doi.org/10.1016/j.molcel.2014.11.009

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, 2014, 'Effects of a Novel Long Noncoding RNA, lncUSMycN, on N-Myc Expression and Neuroblastoma Progression', Journal of the National Cancer Institute, 106, pp. dju113, http://dx.doi.org/10.1093/jnci/dju113

Mattick JS; Dziadek MA; Terrill BN; Kaplan W; Spigelman AD; Bowling FG; Dinger ME, 2014, 'The impact of genomics on the future of medicine and health', Medical Journal of Australia, 201, pp. 17 - 20, http://dx.doi.org/10.5694/mja13.10920

Nguyen TT; Mattick JSA; Yang Q; Orman MA; Ierapetritou MG; Berthiaume F; Androulakis IP, 2014, 'Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver', BMC Bioinformatics, 15, http://dx.doi.org/10.1186/1471-2105-15-83

Cossetti C; Iraci N; Mercer TR; Leonardi T; Alpi E; Drago D; Alfaro-Cervello C; Saini HK; Davis MP; Schaeffer J; Vega B; Stefanini M; Zhao CJ; Muller W; Garcia-Verdugo JM; Mathivanan S; Bachi A; Enright AJ; Mattick JS; Pluchino S, 2014, 'Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells', Molecular Cell, 56, pp. 193 - 204, http://dx.doi.org/10.1016/j.molcel.2014.08.020

Mercer TR; Clark MB; Crawford J; Brunck ME; Gerhardt DJ; Taft RJ; Nielsen LK; Dinger ME; Mattick JS, 2014, 'Targeted sequencing for gene discovery and quantification using RNA CaptureSeq', Nature Protocols, 9, pp. 989 - 1009, http://dx.doi.org/10.1038/nprot.2014.058

Mazar J; Zhao W; Khalil AM; Lee B; Shelley J; Govindarajan SS; Yamamoto F; Ratnam M; Aftab MN; Collins S; Finck BN; Han X; Mattick JS; Dinger ME; Perera RJ, 2014, 'The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells', Oncotarget, 5, pp. 8959 - 8969, http://dx.doi.org/10.18632/oncotarget.1863

Barry G; Briggs JA; Vanichkina DP; Poth EM; Beveridge NJ; Ratnu VS; Nayler SP; Nones K; Hu J; Bredy TW; Nakagawa S; Rigo F; Taft RJ; Cairns MJ; Blackshaw S; Wolvetang EJ; Mattick JS, 2014, 'The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing', Molecular Psychiatry, 19, pp. 486 - 494, http://dx.doi.org/10.1038/mp.2013.45

Morris KV; Mattick JS, 2014, 'The rise of regulatory RNA', Nature Reviews Genetics, 15, pp. 423 - 437, http://dx.doi.org/10.1038/nrg3722

Mattick JS, 2013, 'Probing the phenomics of noncoding RNA', eLife, 2, pp. e01968 - e01968, http://dx.doi.org/10.7554/eLife.01968

Liu G; Mercer TR; Shearwood AMJ; Siira SJ; Hibbs ME; Mattick JS; Rackham O; Filipovska A, 2013, 'Mapping of mitochondrial RNA-protein interactions by digital rnase footprinting', Cell Reports, 5, pp. 839 - 848, http://dx.doi.org/10.1016/j.celrep.2013.09.036

Li JL; Mazar J; Zhong C; Faulkner GJ; Govindarajan SS; Zhang Z; Dinger ME; Meredith G; Adams C; Zhang S; Mattick JS; Ray A; Perera RJ, 2013, 'Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network', Scientific Reports, 3, http://dx.doi.org/10.1038/srep02962

Herschkowitz JI; Coarfa C; Prat A; Toneff MJ; Hoadley KA; Dinger ME; Mattick JS; Mani SA; Perou CM; Rosen JM, 2013, 'The role of long noncoding RNAs in epithelial to mesenchymal transition and cancer stem cells', MOLECULAR CANCER RESEARCH, 11, http://dx.doi.org/10.1158/1557-3125.ADVBC-A039

Smith MA; Gesell T; Stadler PF; Mattick JS, 2013, 'Widespread purifying selection on RNA structure in mammals', Nucleic Acids Research, 41, pp. 8220 - 8236, http://dx.doi.org/10.1093/nar/gkt596

Rakoczy J; Fernandez-Valverde SL; Glazov EA; Wainwright EN; Sato T; Takada S; Combes AN; Korbie DJ; Miller D; Grimmond SM; Little MH; Asahara H; Mattick JS; Taft RJ; Wilhelm D, 2013, 'Micrornas-140-5p/140-3p modulate leydig cell numbers in the developing mouse testis', Biology of Reproduction, 88, http://dx.doi.org/10.1095/biolreprod.113.107607

Mercer TR; Edwards SL; Clark MB; Neph SJ; Wang H; Stergachis AB; John S; Sandstrom R; Li G; Sandhu KS; Ruan Y; Nielsen LK; Mattick JS; Stamatoyannopoulos JA, 2013, 'DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements', Nature Genetics, 45, pp. 852 - 859, http://dx.doi.org/10.1038/ng.2677

Buske FA; Bauer DC; Mattick JS; Bailey TL, 2013, 'Triplex-Inspector: An analysis tool for triplex-mediated targeting of genomic loci', Bioinformatics, 29, pp. 1895 - 1897, http://dx.doi.org/10.1093/bioinformatics/btt315

Liu G; Mattick JS; Taft RJ, 2013, 'A meta-analysis of the genomic and transcriptomic composition of complex life', Cell Cycle, 12, pp. 2061 - 2072, http://dx.doi.org/10.4161/cc.25134

Mattick JSA; Kamisoglu K; Ierapetritou MG; Androulakis IP; Berthiaume F, 2013, 'Branched-chain amino acid supplementation: Impact on signaling and relevance to critical illness', Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 5, pp. 449 - 460, http://dx.doi.org/10.1002/wsbm.1219

Mercer TR; Mattick JS, 2013, 'Understanding the regulatory and transcriptional complexity of the genome through structure', Genome Research, 23, pp. 1081 - 1088, http://dx.doi.org/10.1101/gr.156612.113

Cheetham SW; Gruhl F; Mattick JS; Dinger ME, 2013, 'Long noncoding RNAs and the genetics of cancer', British Journal of Cancer, 108, pp. 2419 - 2425, http://dx.doi.org/10.1038/bjc.2013.233

Clark MB; Choudhary A; Smith MA; Taft RJ; Mattick JS, 2013, 'The dark matter rises: The expanding world of regulatory RNAs', Essays in Biochemistry, 54, pp. 1 - 16, http://dx.doi.org/10.1042/BSE0540001

Amaral PP; Dinger ME; Mattick JS, 2013, 'Non-coding RNAs in homeostasis, disease and stress responses: An evolutionary perspective', Briefings in Functional Genomics, 12, pp. 254 - 278, http://dx.doi.org/10.1093/bfgp/elt016

Cattenoz PB; Taft RJ; Westhof E; Mattick JS, 2013, 'Transcriptome-wide identification of A > i RNA editing sites by inosine specific cleavage', RNA, 19, pp. 257 - 270, http://dx.doi.org/10.1261/rna.036202.112

Plummer PN; Freeman R; Taft RJ; Vider J; Sax M; Umer BA; Gao D; Johns C; Mattick JS; Wilton SD; Ferro V; McMillan NAJ; Swarbrick A; Mittal V; Mellick AS, 2013, 'MicroRNAs regulate tumor angiogenesis modulated by endothelial progenitor cells', Cancer Research, 73, pp. 341 - 352, http://dx.doi.org/10.1158/0008-5472.CAN-12-0271

Marcellin E; Mercer TR; Licona-Cassani C; Palfreyman RW; Dinger ME; Steen JA; Mattick JS; Nielsen LK, 2013, 'Saccharopolyspora erythraea’s genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch', BMC Genomics, 14, pp. 15 - 25, http://dx.doi.org/10.1186/1471-2164-14-15

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