By Professor John Stanley Mattick

Journal articles

Smart CE; Askarian-amiri ME; Wronski A; Dinger ME; Crawford JA; Ovchinnikov DA; Vargas AC; Reid LE; Simpson PT; Song S; Wiesner C; French JD; Dave RK; da Silva L; Purdon AS; Andrew M; Mattick JS; Lakhani SR; Brown MA; Kellie S, 2012, 'Expression and function of the protein tyrosine phosphatase receptor J (PTPRJ) in normal mammary epithelial cells and breast tumors', PLoS One, 7, pp. e40742, http://dx.doi.org/10.1371/journal.pone.0040742

Clark M; Johnston RL; Inostroza-Ponta M; Fox AH; Fortini E; Moscato P; Dinger ME; Mattick JS, 2012, 'Genome-wide analysis of long noncoding RNA stability', Genome Research, 22, pp. 885 - 898, http://dx.doi.org/10.1101/gr.131037.111

Schonrock N; Harvey RP; Mattick JS, 2012, 'Long noncoding RNAs in cardiac development and pathophysiology', Circulation Research, 111, pp. 1349 - 1362, http://dx.doi.org/10.1161/CIRCRESAHA.112.268953

Gascoigne DK; Cheetham SW; Cattenoz PB; Clark M; Amaral PP; Taft R; Wilhelm D; Dinger ME; Mattick JS, 2012, 'Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes', Bioinformatics, 28, pp. 3042 - 3050, http://dx.doi.org/10.1093/bioinformatics/bts582

Pineda SS; Wilson D; Mattick JS; King G, 2012, 'The lethal toxin from Australian funnel-web spiders is encoded by an intronless gene', PLoS One, 7, pp. Article numbere43699, http://dx.doi.org/10.1371/journal.pone.0043699

Barry G; Mattick JS, 2012, 'The role of regulatory RNA in cognitive evolution', Trends in Cognitive Sciences, 16, pp. 497 - 503, http://dx.doi.org/10.1016/j.tics.2012.08.007

Buske FA; Bauer DC; Mattick JS; Bailey T, 2012, 'Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data', Genome Research, 22, pp. 1372 - 1381, http://dx.doi.org/10.1101/gr.130237.111

Rackham O; Shearwood AMJ; Mercer TR; Davies SMK; Mattick JS; Filipovska A, 2011, 'Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins', RNA, 17, pp. 2085 - 2093, http://dx.doi.org/10.1261/rna.029405.111

Baillie JK; Barnett MW; Upton KR; Gerhardt DJ; Richmond TA; De Sapio F; Brennan P; Rizzu P; Smith S; Fell M; Talbot RT; Gustincich S; Freeman TC; Mattick JS; Hume DA; Heutink P; Carninci P; Jeddeloh JA; Faulkner GJ, 2011, 'Somatic retrotransposition alters the genetic landscape of the human brain', Nature, 479, pp. 534 - 537, http://dx.doi.org/10.1038/nature10531

Mattick JS, 2011, 'RNA Networks as Digital Control Circuits of Nuclear Functions', , pp. 353 - 363, http://dx.doi.org/10.1002/9783527639991.ch14

Mattick JS, 2011, 'The double life of RNA', Biochimie, 93, http://dx.doi.org/10.1016/S0300-9084(11)00355-5

Mattick JS, 2011, 'The double life of RNA', BIOCHIMIE, 93, pp. VIII - IX, http://dx.doi.org/10.1016/S0300-9084(11)00355-5

Mattick JS; Clark MB, 2011, 'RNA lights up', Nature Biotechnology, 29, pp. 883 - 884, http://dx.doi.org/10.1038/nbt.2003

Mattick JS, 2011, 'The hidden layer of RNA regulation underpinning human development and cognition', JOURNAL OF INTELLECTUAL DISABILITY RESEARCH, 55, pp. 948 - 948, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000295184700005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Thiagarajan RD; Cloonan N; Gardiner BB; Mercer TR; Kolle G; Nourbakhsh E; Wani S; Tang D; Krishnan K; Georgas KM; Rumballe BA; Chiu HS; Steen JA; Mattick JS; Little MH; Grimmond SM, 2011, 'Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling', BMC Genomics, 12, http://dx.doi.org/10.1186/1471-2164-12-441

Lopez Sanchez MIG; Mercer TR; Davies SMK; Shearwood AMJ; Nygård KKA; Richman TR; Mattick JS; Rackham O; Filipovska A, 2011, 'RNA processing in human mitochondria', Cell Cycle, 10, pp. 2904 - 2916, http://dx.doi.org/10.4161/cc.10.17.17060

Mercer TR; Neph S; Dinger ME; Crawford J; Smith MA; Shearwood AMJ; Haugen E; Bracken CP; Rackham O; Stamatoyannopoulos JA; Filipovska A; Mattick JS, 2011, 'The human mitochondrial transcriptome', Cell, 146, pp. 645 - 658, http://dx.doi.org/10.1016/j.cell.2011.06.051

Faunes F; Sanchez N; Moreno M; Olivares GH; Lee-Liu D; Almonacid L; Slater AW; Norambuena T; Taft RJ; Mattick JS; Melo F; Larrain J, 2011, 'Expression of transposable elements in neural tissues during Xenopus development', PLoS ONE, 6, http://dx.doi.org/10.1371/journal.pone.0022569

Bracken CP; Szubert JM; Mercer TR; Dinger ME; Thomson DW; Mattick JS; Michael MZ; Goodall GJ, 2011, 'Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage', Nucleic Acids Research, 39, pp. 5658 - 5668, http://dx.doi.org/10.1093/nar/gkr110

Bredy TW; Lin Q; Wei W; Baker-Andresen D; Mattick JS, 2011, 'MicroRNA regulation of neural plasticity and memory', Neurobiology of Learning and Memory, 96, pp. 89 - 94, http://dx.doi.org/10.1016/j.nlm.2011.04.004

Fernandez-Valverde SL; Taft RJ; Mattick JS, 2011, 'MicroRNAs in β-cell biology, insulin resistance, diabetes and its complications', Diabetes, 60, pp. 1825 - 1831, http://dx.doi.org/10.2337/db11-0171

Mattick JS, 2011, 'The central role of RNA in human development and cognition', FEBS Letters, 585, pp. 1600 - 1616, http://dx.doi.org/10.1016/j.febslet.2011.05.001

Khaitan D; Dinger ME; Mazar J; Crawford J; Smith MA; Mattick JS; Perera RJ, 2011, 'The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion', Cancer Research, 71, pp. 3852 - 3862, http://dx.doi.org/10.1158/0008-5472.CAN-10-4460

Wong CE; Zhao YT; Wang XJ; Croft L; Wang ZH; Haerizadeh F; Mattick JS; Singh MB; Carroll BJ; Bhalla PL, 2011, 'MicroRNAs in the shoot apical meristem of soybean', Journal of Experimental Botany, 62, pp. 2495 - 2506, http://dx.doi.org/10.1093/jxb/erq437

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, 2011, 'SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer', RNA, 17, pp. 878 - 891, http://dx.doi.org/10.1261/rna.2528811

Mercer TR; Wilhelm D; Dinger ME; Soldà G; Korbie DJ; Glazov EA; Truong V; Schwenke M; Simons C; Matthaei KI; Saint R; Koopman P; Mattick JS, 2011, 'Expression of distinct RNAs from 3′ untranslated regions', Nucleic Acids Research, 39, pp. 2393 - 2403, http://dx.doi.org/10.1093/nar/gkq1158

Mattick JS, 2011, 'Genome-sequencing anniversary. The genomic foundation is shifting.', Science (New York, N.Y.), 331, pp. 874, http://dx.doi.org/10.1126/science.1203703

Amaral PP; Clark MB; Gascoigne DK; Dinger ME; Mattick JS, 2011, 'LncRNAdb: A reference database for long noncoding RNAs', Nucleic Acids Research, 39, http://dx.doi.org/10.1093/nar/gkq1138

Mattick JS, 2011, 'Long noncoding RNAs in cell and developmental biology', Seminars in Cell and Developmental Biology, 22, pp. 327, http://dx.doi.org/10.1016/j.semcdb.2011.05.002

Clark MB; Mattick JS, 2011, 'Long noncoding RNAs in cell biology', Seminars in Cell and Developmental Biology, 22, pp. 366 - 376, http://dx.doi.org/10.1016/j.semcdb.2011.01.001

Buske FA; Mattick JS; Bailey TL, 2011, 'Potential in vivo roles of nucleic acid triple-helices', RNA Biology, 8, pp. 427 - 439, http://dx.doi.org/10.4161/rna.8.3.14999

Dinger ME; Gascoigne DK; Mattick JS, 2011, 'The evolution of RNAs with multiple functions', Biochimie, 93, pp. 2013 - 2018, http://dx.doi.org/10.1016/j.biochi.2011.07.018

Clark MB; Amaral PP; Schlesinger FJ; Dinger ME; Taft R; Rinn JL; Ponting CP; Stadler PF; Morris K; Morillon A; Rozowsky JS; Gerstein MB; Wahlestedt C; Hayashizaki Y; Carninci P; Gingeras TR; Mattick JS, 2011, 'The reality of pervasive transcription', PLoS Biology, 9, pp. e1000625, http://dx.doi.org/10.1371/journal.pbio.1000625

Taft R; Hawkins PG; Mattick JS; Morris K, 2011, 'The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization', Epigenetics & Chromatin, 4, pp. 1 - 13, http://www.ncbi.nlm.nih.gov/pubmed/21813016;%20http://www.epigeneticsandchromatin.com/content/pdf/1756-8935-4-13.pdf

Mercer TR; Dinger ME; Bracken CP; Kolle G; Szubert JM; Korbie DJ; Askarian-Amiri ME; Gardiner BB; Goodall GJ; Grimmond SM; Mattick JS, 2010, 'Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome', Genome Research, 20, pp. 1639 - 1650, http://dx.doi.org/10.1101/gr.112128.110

Mattick JS, 2010, 'Linc-ing long noncoding RNAs and enhancer function', Developmental Cell, 19, pp. 485 - 486, http://dx.doi.org/10.1016/j.devcel.2010.10.003

Mattick JS, 2010, 'The central role of RNA in the genetic programming of complex organisms', Anais da Academia Brasileira de Ciencias, 82, pp. 933 - 939, http://dx.doi.org/10.1590/S0001-37652010000400016

Aung HT; Harrison DK; Findlay I; Mattick JS; Martin NG; Carroll BJ, 2010, 'Stringent programming of DNA methylation in humans', Twin Research and Human Genetics, 13, pp. 405 - 411, http://dx.doi.org/10.1375/twin.13.5.405

Jung CH; Makunin IV; Mattick JS, 2010, 'Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs', Genomics, 96, pp. 154 - 166, http://dx.doi.org/10.1016/j.ygeno.2010.05.006

Taft RJ; Simons C; Nahkuri S; Oey H; Korbie DJ; Mercer TR; Holst J; Ritchie W; Wong JJL; Rasko JEJ; Rokhsar DS; Degnan BM; Mattick JS, 2010, 'Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans', Nature Structural and Molecular Biology, 17, pp. 1030 - 1034, http://dx.doi.org/10.1038/nsmb.1841

Mattick J, 2010, 'Video Q&A: Non-coding RNAs and eukaryotic evolution - a personal view', BMC Biology, 8, http://dx.doi.org/10.1186/1741-7007-8-67

Mazar J; Sinha S; Dinger ME; Mattick JS; Perera RJ, 2010, 'Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent', Molecular Genetics and Genomics, 284, pp. 1 - 9, http://dx.doi.org/10.1007/s00438-010-0543-6

Mattick JS, 2010, 'RNA as the substrate for epigenome-environment interactions (BioEssays)', BioEssays, 32, pp. 642, http://dx.doi.org/10.1002/bies.201090026

Mattick JS, 2010, 'RNA as the substrate for epigenome-environment interactions: RNA guidance of epigenetic processes and the expansion of RNA editing in animals underpins development, phenotypic plasticity, learning, and cognition', BioEssays, 32, pp. 548 - 552, http://dx.doi.org/10.1002/bies.201000028

Qureshi IA; Mattick JS; Mehler MF, 2010, 'Long non-coding RNAs in nervous system function and disease', Brain Research, 1338, pp. 20 - 35, http://dx.doi.org/10.1016/j.brainres.2010.03.110

Lai J; Lehman ML; Dinger ME; Hendy SC; Mercer TR; Seim I; Lawrence MG; Mattick JS; Clements JA; Nelson CC, 2010, 'A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells', RNA, 16, pp. 1156 - 1166, http://dx.doi.org/10.1261/rna.2019810

Oldmeadow C; Mengersen K; Mattick JS; Keith JM, 2010, 'Multiple evolutionary rate classes in animal genome evolution', Molecular Biology and Evolution, 27, pp. 942 - 953, http://dx.doi.org/10.1093/molbev/msp299

Mercer TR; Qureshi IA; Gokhan S; Dinger ME; Li G; Mattick JS; Mehler MF, 2010, 'Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation', BMC Neuroscience, 11, http://dx.doi.org/10.1186/1471-2202-11-14

De Hoon MJL; Taft RJ; Hashimoto T; Kanamori-Katayama M; Kawaji H; Kawano M; Kishima M; Lassmann T; Faulkner GJ; Mattick JS; Daub CO; Carninci P; Kawai J; Suzuki H; Hayashizaki Y, 2010, 'Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries', Genome Research, 20, pp. 257 - 264, http://dx.doi.org/10.1101/gr.095273.109

Jung CH; Hansen MA; Makunin IV; Korbie DJ; Mattick JS, 2010, 'Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data', BMC Genomics, 11, http://dx.doi.org/10.1186/1471-2164-11-77

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