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Items: 1 to 50 of 274

1.

Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing.

Mattick JS, Dinger M, Schonrock N, Cowley M.

Med J Aust. 2018 Apr 9. [Epub ahead of print] No abstract available.

PMID:
29621958
2.

Universal Alternative Splicing of Noncoding Exons.

Deveson IW, Brunck ME, Blackburn J, Tseng E, Hon T, Clark TA, Clark MB, Crawford J, Dinger ME, Nielsen LK, Mattick JS, Mercer TR.

Cell Syst. 2018 Feb 28;6(2):245-255.e5. doi: 10.1016/j.cels.2017.12.005. Epub 2018 Jan 24.

PMID:
29396323
3.

DotAligner: identification and clustering of RNA structure motifs.

Smith MA, Seemann SE, Quek XC, Mattick JS.

Genome Biol. 2017 Dec 28;18(1):244. doi: 10.1186/s13059-017-1371-3.

4.

Intergenic disease-associated regions are abundant in novel transcripts.

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.

Genome Biol. 2017 Dec 28;18(1):241. doi: 10.1186/s13059-017-1363-3.

5.

Prioritising the application of genomic medicine.

Doble B, Schofield DJ, Roscioli T, Mattick JS.

NPJ Genom Med. 2017 Nov 21;2:35. doi: 10.1038/s41525-017-0037-0. eCollection 2017. Review.

6.

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework.

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.

Adv Exp Med Biol. 2017;1031:55-94. doi: 10.1007/978-3-319-67144-4_4.

PMID:
29214566
7.

The RNA modification landscape in human disease.

Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM.

RNA. 2017 Dec;23(12):1754-1769. doi: 10.1261/rna.063503.117. Epub 2017 Aug 30. Review.

PMID:
28855326
8.

Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination.

Deveson IW, Holleley CE, Blackburn J, Marshall Graves JA, Mattick JS, Waters PD, Georges A.

Sci Adv. 2017 Jun 14;3(6):e1700731. doi: 10.1126/sciadv.1700731. eCollection 2017 Jun.

9.

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome.

Deveson IW, Hardwick SA, Mercer TR, Mattick JS.

Trends Genet. 2017 Jul;33(7):464-478. doi: 10.1016/j.tig.2017.04.004. Epub 2017 May 20. Review.

PMID:
28535931
10.

Charting the unknown epitranscriptome.

Novoa EM, Mason CE, Mattick JS.

Nat Rev Mol Cell Biol. 2017 Jun;18(6):339-340. doi: 10.1038/nrm.2017.49. Epub 2017 May 10.

PMID:
28488699
11.

Initiating an undiagnosed diseases program in the Western Australian public health system.

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.

Orphanet J Rare Dis. 2017 May 3;12(1):83. doi: 10.1186/s13023-017-0619-z.

12.

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.

Robinson KM, Crabtree J, Mattick JS, Anderson KE, Dunning Hotopp JC.

Microbiome. 2017 Jan 25;5(1):9. doi: 10.1186/s40168-016-0224-8.

13.

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states.

Barry G, Briggs JA, Hwang DW, Nayler SP, Fortuna PR, Jonkhout N, Dachet F, Maag JL, 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.

Sci Rep. 2017 Jan 5;7:40127. doi: 10.1038/srep40127.

14.

Structural and Functional Annotation of Long Noncoding RNAs.

Smith MA, Mattick JS.

Methods Mol Biol. 2017;1526:65-85.

PMID:
27896736
15.

Spliced synthetic genes as internal controls in RNA sequencing experiments.

Hardwick SA, Chen WY, Wong T, Deveson IW, Blackburn J, Andersen SB, Nielsen LK, Mattick JS, Mercer TR.

Nat Methods. 2016 Sep;13(9):792-8. doi: 10.1038/nmeth.3958. Epub 2016 Aug 8.

PMID:
27502218
16.

Representing genetic variation with synthetic DNA standards.

Deveson IW, Chen WY, Wong T, Hardwick SA, Andersen SB, Nielsen LK, Mattick JS, Mercer TR.

Nat Methods. 2016 Sep;13(9):784-91. doi: 10.1038/nmeth.3957. Epub 2016 Aug 8.

PMID:
27502217
17.

The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation.

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.

Sci Rep. 2016 May 26;6:26657. doi: 10.1038/srep26657.

18.

Seq and You Will Find.

Schonrock N, Jonkhout N, Mattick JS.

Curr Gene Ther. 2016;16(3):220-9. Review.

PMID:
27216913
19.

Improved definition of the mouse transcriptome via targeted RNA sequencing.

Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ.

Genome Res. 2016 May;26(5):705-16. doi: 10.1101/gr.199760.115.

20.

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

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.

Cell. 2016 May 19;165(5):1267-1279. doi: 10.1016/j.cell.2016.04.028. Epub 2016 May 12.

21.

The promise of personalised medicine.

Doble B, Schofield DJ, Roscioli T, Mattick JS.

Lancet. 2016 Jan 30;387(10017):433-4. doi: 10.1016/S0140-6736(16)00176-8. No abstract available.

PMID:
26869572
22.

The Long Noncoding RNA SPRIGHTLY Regulates Cell Proliferation in Primary Human Melanocytes.

Zhao W, Mazar J, Lee B, Sawada J, Li JL, Shelley J, Govindarajan S, Towler D, Mattick JS, Komatsu M, Dinger ME, Perera RJ.

J Invest Dermatol. 2016 Apr;136(4):819-28. doi: 10.1016/j.jid.2016.01.018. Epub 2016 Jan 29.

23.

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution.

Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G.

Neuron. 2015 Dec 2;88(5):861-877. doi: 10.1016/j.neuron.2015.09.045. Review.

24.

Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice.

Spadaro PA, Flavell CR, Widagdo J, Ratnu VS, Troup M, Ragan C, Mattick JS, Bredy TW.

Biol Psychiatry. 2015 Dec 15;78(12):848-59. doi: 10.1016/j.biopsych.2015.02.004. Epub 2015 Feb 11.

25.

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

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.

Nat Methods. 2015 Apr;12(4):339-42. doi: 10.1038/nmeth.3321. Epub 2015 Mar 9.

PMID:
25751143
26.

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.

Londin E, Loher P, Telonis AG, Quann K, Clark P, Jing Y, Hatzimichael E, Kirino Y, Honda S, Lally M, Ramratnam B, Comstock CE, 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.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1106-15. doi: 10.1073/pnas.1420955112. Epub 2015 Feb 23.

27.

Discovery and annotation of long noncoding RNAs.

Mattick JS, Rinn JL.

Nat Struct Mol Biol. 2015 Jan;22(1):5-7. doi: 10.1038/nsmb.2942.

PMID:
25565026
28.

Genome-wide discovery of human splicing branchpoints.

Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS.

Genome Res. 2015 Feb;25(2):290-303. doi: 10.1101/gr.182899.114. Epub 2015 Jan 5.

29.

Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms.

Werner A, Piatek MJ, Mattick JS.

Ann N Y Acad Sci. 2015 Apr;1341:156-63. doi: 10.1111/nyas.12608. Epub 2014 Dec 31.

30.

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells.

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.

Oncotarget. 2014 Oct 15;5(19):8959-69.

31.

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.

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 C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS, Pluchino S.

Mol Cell. 2014 Oct 23;56(2):193-204. doi: 10.1016/j.molcel.2014.08.020. Epub 2014 Sep 18. Erratum in: Mol Cell. 2014 Nov 20;56(4):609.

32.

The impact of genomics on the future of medicine and health.

Mattick JS, Dziadek MA, Terrill BN, Kaplan W, Spigelman AD, Bowling FG, Dinger ME.

Med J Aust. 2014 Jul 7;201(1):17-20. No abstract available.

PMID:
24999876
33.

Effects of a novel long noncoding RNA, lncUSMycN, on N-Myc expression and neuroblastoma progression.

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.

J Natl Cancer Inst. 2014 Jun 6;106(7). pii: dju113. doi: 10.1093/jnci/dju113. Print 2014 Jul. Erratum in: J Natl Cancer Inst. 2015 Jan;107(1):doi/10.1093/jnci/dju359.

PMID:
24906397
34.

The rise of regulatory RNA.

Morris KV, Mattick JS.

Nat Rev Genet. 2014 Jun;15(6):423-37. doi: 10.1038/nrg3722. Epub 2014 Apr 29. Review.

35.

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS.

Nat Protoc. 2014 May;9(5):989-1009. doi: 10.1038/nprot.2014.058. Epub 2014 Apr 3.

PMID:
24705597
36.

Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver.

Nguyen TT, Mattick JS, Yang Q, Orman MA, Ierapetritou MG, Berthiaume F, Androulakis IP.

BMC Bioinformatics. 2014 Mar 25;15:83. doi: 10.1186/1471-2105-15-83.

37.

Probing the phenomics of noncoding RNA.

Mattick JS.

Elife. 2013 Dec 31;2:e01968. doi: 10.7554/eLife.01968.

38.

Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting.

Liu G, Mercer TR, Shearwood AM, Siira SJ, Hibbs ME, Mattick JS, Rackham O, Filipovska A.

Cell Rep. 2013 Nov 14;5(3):839-48. doi: 10.1016/j.celrep.2013.09.036. Epub 2013 Oct 31.

39.

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network.

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.

Sci Rep. 2013 Oct 16;3:2962. doi: 10.1038/srep02962.

40.

Topology and dynamics of signaling networks: in search of transcriptional control of the inflammatory response.

Androulakis IP, Kamisoglu K, Mattick JS.

Annu Rev Biomed Eng. 2013;15:1-28. doi: 10.1146/annurev-bioeng-071812-152425. Review.

PMID:
23862674
41.

Widespread purifying selection on RNA structure in mammals.

Smith MA, Gesell T, Stadler PF, Mattick JS.

Nucleic Acids Res. 2013 Sep;41(17):8220-36. doi: 10.1093/nar/gkt596. Epub 2013 Jul 11.

42.

The dark matter rises: the expanding world of regulatory RNAs.

Clark MB, Choudhary A, Smith MA, Taft RJ, Mattick JS.

Essays Biochem. 2013;54:1-16. doi: 10.1042/bse0540001. Review.

PMID:
23829523
43.

Understanding the regulatory and transcriptional complexity of the genome through structure.

Mercer TR, Mattick JS.

Genome Res. 2013 Jul;23(7):1081-8. doi: 10.1101/gr.156612.113. Review.

44.

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.

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.

Nat Genet. 2013 Aug;45(8):852-9. doi: 10.1038/ng.2677. Epub 2013 Jun 23.

45.

A meta-analysis of the genomic and transcriptomic composition of complex life.

Liu G, Mattick JS, Taft RJ.

Cell Cycle. 2013 Jul 1;12(13):2061-72. doi: 10.4161/cc.25134. Epub 2013 Jun 6.

46.

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Buske FA, Bauer DC, Mattick JS, Bailey TL.

Bioinformatics. 2013 Aug 1;29(15):1895-7. doi: 10.1093/bioinformatics/btt315. Epub 2013 Jun 5.

47.

Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective.

Amaral PP, Dinger ME, Mattick JS.

Brief Funct Genomics. 2013 May;12(3):254-78. doi: 10.1093/bfgp/elt016. Review.

PMID:
23709461
48.

Long noncoding RNAs and the genetics of cancer.

Cheetham SW, Gruhl F, Mattick JS, Dinger ME.

Br J Cancer. 2013 Jun 25;108(12):2419-25. doi: 10.1038/bjc.2013.233. Epub 2013 May 9. Review.

49.

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing.

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.

Mol Psychiatry. 2014 Apr;19(4):486-94. doi: 10.1038/mp.2013.45. Epub 2013 Apr 30.

PMID:
23628989
50.

MicroRNAs-140-5p/140-3p modulate Leydig cell numbers in the developing mouse testis.

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.

Biol Reprod. 2013 Jun 6;88(6):143. doi: 10.1095/biolreprod.113.107607. Print 2013 Jun.

PMID:
23616593

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