Selected Publications

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. The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation. Sci Rep. 2016; May 26;6:26657.

Schonrock N, Jonkhout N, Mattick JS. Seq and you will find. Curr Gene Ther. 2016 May 24. [Epub ahead of print] PubMed PMID: 27216913.

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. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016; May 19;165(5):1267-79.

Doble B, Schofield DJ, Roscioli T, Mattick JS. The promise of personalised medicine. Lancet. 2016; Jan 30;387(10017):433-4.

Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G. Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution. Neuron. 2015; Dec 2;88(5):861-77.

Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME. Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods. 2015; Apr;12(4):339-42.

Mattick JS, Rinn JL. Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol. 2015; Jan;22(1):5-7.

Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Genome-wide discovery of human splicing branchpoints. Genome Res. 2015; Feb;25(2):290-303.

Mattick JS, Dziadek MA, Terrill BN, Kaplan W, Spigelman AD, Bowling FG, Dinger ME. The impact of genomics on the future of medicine and health. Med J Aust. 2014; Jul 7;201(1):17-20. 

Werner A, Piatek MJ, Mattick JS. Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms. Ann N Y Acad Sci. 2015; Apr;1341:156-63.

Morris KV, Mattick JS. The rise of regulatory RNA. Nat Rev Genet. 2014; Jun;15(6):423-37.

Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc. 2014; May;9(5):989-1009.

Mattick JS. Probing the phenomics of noncoding RNA. Elife. 2013; Dec 31;2:e01968.

Liu G, Mercer TR, Shearwood AM, Siira SJ, Hibbs ME, Mattick JS, Rackham O, Filipovska A. Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting. Cell Rep. 2013; Nov 14;5(3):839-48.

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. Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Sci Rep. 2013; Oct 16;3:2962.

Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res. 2013; Sep;41(17):8220-36.

Clark MB, Choudhary A, Smith MA, Taft RJ, Mattick JS. The dark matter rises: the expanding world of regulatory RNAs. Essays Biochem. 2013;54:1-16.

Liu G, Mattick JS, Taft RJ. A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle. 2013; Jul 1;12(13):2061-72.

Mercer TR, Mattick JS. Understanding the regulatory and transcriptional complexity of the genome through structure. Genome Res. 2013; Jul;23(7):1081-8.

Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res. 2013; 41(17):8220-36.

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. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet. 2013; 45(8):852-9.

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. The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry. 2013 Apr 30. doi: 10.1038/mp.2013.45. [Epub ahead of print]

Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013; 20(3):300-7. Review.

Cattenoz PB, Taft RJ, Westhof E, Mattick JS. Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage. RNA. 2013; 19(2):257-70.

Barry G, Mattick JS. The role of regulatory RNA in cognitive evolution. Trends Cogn Sci. 2012; 16(10):497-503.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2011; 30(1):99-104.

Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, Filipovska A, Mattick JS. The human mitochondrial transcriptome. Cell. 2011; 146(4):645-58.

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS. The reality of pervasive transcription. PLoS Biol. 2011; 9(7):e1000625; discussion e1001102.

Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME, Mattick JS. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA. 2011; 17(5):878-91.

Mattick JS The central role of RNA in human development and cognition. FEBS Letters 2011; 585:1600–1616.

Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME and Mattick JS. Genome-wide analysis of long noncoding RNA stability. Genome Research 2012; 22: 885-898.

Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ-L, Rasko JEJ, Rokhsar DS, Degnan BM and Mattick JS. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Structural and Molecular Biology 2010; 17:1030-1034.

Mercer TR, Dinger ME, Sunkin SM, Mehler MF and Mattick JS. Specific expression of non-coding RNAs in mouse brain. Proceedings of the National Academy of Sciences USA 2008; 105:716-721.

Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC and Mattick JS. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Research 2008; 18:1433–1445.

Amaral PP, Dinger ME, Mercer TR and Mattick JS. The eukaryotic genome as an RNA machine. Science 2008; 319:1787-1789.

Pheasant M and Mattick JS. Raising the estimate of functional human sequences. Genome Research 2007; 17:1245-1253.

Taft RJ, Pheasant M and Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007; 29:288-299.

Bejerano G, Pheasant M, Makunin IV, Stephen S, Kent WJ, Mattick JS and Haussler D. Ultra-conserved elements in the human genome. Science 2004; 304:1321-1325.

Mattick JS. RNA regulation: a new genetics? Nature Reviews Genetics 2004; 5:316-323.


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