By Professor John Stanley Mattick

Journal articles

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

Mattick JS; Taft RJ; Faulkner GJ, 2010, 'A global view of genomic information - moving beyond the gene and the master regulator', Trends in Genetics, 26, pp. 21 - 28, http://dx.doi.org/10.1016/j.tig.2009.11.002

Fernandez-Valverde SL; Taft RJ; Mattick JS, 2010, 'Dynamic isomiR regulation in Drosophila development', RNA, 16, pp. 1881 - 1888, http://dx.doi.org/10.1261/rna.2379610

Taft RJ; Pang KC; Mercer TR; Dinger M; Mattick JS, 2010, 'Non-coding RNAs: Regulators of disease', Journal of Pathology, 220, pp. 126 - 139, http://dx.doi.org/10.1002/path.2638

Amaral PP; Neyt C; Wilkins SJ; Askarian-Amiri ME; Sunkin SM; Perkins AC; Mattick JS, 2009, 'Complex architecture and regulated expression of the Sox2ot locus during vertebrate development', RNA, 15, pp. 2013 - 2027, http://dx.doi.org/10.1261/rna.1705309

Nahkuri S; Taft RJ; Mattick JS, 2009, 'Nucleosomes are preferentially positioned at exons in somatic and sperm cells', Cell Cycle, 8, pp. 3420 - 3424, http://dx.doi.org/10.4161/cc.8.20.9916

Dinger ME; Amaral PP; Mercer TR; Mattick JS, 2009, 'Pervasive transcription of the eukaryotic genome: Functional indices and conceptual implications', Briefings in Functional Genomics and Proteomics, 8, pp. 407 - 423, http://dx.doi.org/10.1093/bfgp/elp038

Taft RJ; Kaplan CD; Simons C; Mattick JS, 2009, 'Evolution, biogenesis and function of promoter-associated RNAs', Cell Cycle, 8, pp. 2332 - 2338, http://dx.doi.org/10.4161/cc.8.15.9154

Mattick JS, 2009, 'Has evolution learnt how to learn?', EMBO Reports, 10, pp. 665, http://dx.doi.org/10.1038/embor.2009.135

Taft RJ; Glazov EA; Cloonan N; Simons C; Stephen S; Faulkner GJ; Lassmann T; Forrest ARR; Grimmond SM; Schroder K; Irvine K; Arakawa T; Nakamura M; Kubosaki A; Hayashida K; Kawazu C; Murata M; Nishiyori H; Fukuda S; Kawai J; Daub CO; Hume DA; Suzuki H; Orlando V; Carninci P; Hayashizaki Y; Mattick JS, 2009, 'Erratum: Tiny RNAs associated with transcription start sites in animals (Nature Genetics (2009) 41 (572-578)).', Nature Genetics, 41, pp. 859, http://dx.doi.org/10.1038/ng0709-859a

Taft RJ; Glazov EA; Lassmann T; Hayashizaki Y; Carninci P; Mattick JS, 2009, 'Small RNAs derived from snoRNAs', RNA, 15, pp. 1233 - 1240, http://dx.doi.org/10.1261/rna.1528909

Pang KC; Dinger ME; Mercer TR; Malquori L; Grimmond SM; Chen W; Mattick JS, 2009, 'Genome-wide identification of long noncoding RNAs in CD8⁺ T cells', Journal of Immunology, 182, pp. 7738 - 7748, http://dx.doi.org/10.4049/jimmunol.0900603

Mattick J, 2009, 'Junk no more - Rnas get networking', Australian Life Scientist, 6, pp. 6 - 10

Suzuki H; Forrest ARR; Van Nimwegen E; Daub CO; Balwierz PJ; Irvine KM; Lassmann T; Ravasi T; Hasegawa Y; De Hoon MJL; Katayama S; Schroder K; Carninci P; Tomaru Y; Kanamori-Katayama M; Kubosaki A; Akalin A; Ando Y; Arner E; Asada M; Asahara H; Bailey T; Bajic VB; Bauer D; Beckhouse AG; Bertin N; Björkegren J; Brombacher F; Bulger E; Chalk AM; Chiba J; Cloonan N; Dawe A; Dostie J; Engström PG; Essack M; Faulkner GJ; Fink JL; Fredman D; Fujimori K; Furuno M; Gojobori T; Gough J; Grimmond SM; Gustafsson M; Hashimoto M; Hashimoto T; Hatakeyama M; Heinzel S; Hide W; Hofmann O; Hörnquist M; Huminiecki L; Ikeo K; Imamoto N; Inoue S; Inoue Y; Ishihara R; Iwayanagi T; Jacobsen A; Kaur M; Kawaji H; Kerr MC; Kimura R; Kimura S; Kimura Y; Kitano H; Koga H; Kojima T; Kondo S; Konno T; Krogh A; Kruger A; Kumar A; Lenhard B; Lennartsson A; Lindow M; Lizio M; MacPherson C; Maeda N; Maher CA; Maqungo M; Mar J; Matigian NA; Matsuda H; Mattick JS; Meier S; Miyamoto S; Miyamoto-Sato E; Nakabayashi K; Nakachi Y; Nakano M; Nygaard S; Okayama T; Okazaki Y; Okuda-Yabukami H; Orlando V; Otomo J; Pachkov M; Petrovsky N, 2009, 'The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line', Nature Genetics, 41, pp. 553 - 562, http://dx.doi.org/10.1038/ng.375

Taft RJ; Glazov EA; Cloonan N; Simons C; Stephen S; Faulkner GJ; Lassmann T; Forrest ARR; Grimmond SM; Schroder K; Irvine K; Arakawa T; Nakamura M; Kubosaki A; Hayashida K; Kawazu C; Murata M; Nishiyori H; Fukuda S; Kawai J; Daub CO; Hume DA; Suzuki H; Orlando V; Carninci P; Hayashizaki Y; Mattick JS, 2009, 'Tiny RNAs associated with transcription start sites in animals', Nature Genetics, 41, pp. 572 - 578, http://dx.doi.org/10.1038/ng.312

Guffanti A; Iacono M; Pelucchi P; Kim N; Soldà G; Croft LJ; Taft RJ; Rizzi E; Askarian-Amiri M; Bonnal RJ; Callari M; Mignone F; Pesole G; Bertalot G; Bernardi L; Albertini A; Lee C; Mattick JS; Zucchi I; De Bellis G, 2009, 'A transcriptional sketch of a primary human breast cancer by 454 deep sequencing', BMC Genomics, 10, http://dx.doi.org/10.1186/1471-2164-10-163

Mattick JS, 2009, 'The genetic signatures of noncoding RNAs', PLoS Genetics, 5, http://dx.doi.org/10.1371/journal.pgen.1000459

Mercer TR; Dinger ME; Mattick JS, 2009, 'Long non-coding RNAs: Insights into functions', Nature Reviews Genetics, 10, pp. 155 - 159, http://dx.doi.org/10.1038/nrg2521

Sunwoo H; Dinger ME; Wilusz JE; Amaral PP; Mattick JS; Spector DL, 2009, 'Men ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles', Genome Research, 19, pp. 347 - 359, http://dx.doi.org/10.1101/gr.087775.108

Webster RJ; Giles KM; Price KJ; Zhang PM; Mattick JS; Leedman PJ, 2009, 'Regulation of epidermal growth factor receptor signaling in human cancer cells by MicroRNA-7', Journal of Biological Chemistry, 284, pp. 5731 - 5741, http://dx.doi.org/10.1074/jbc.M804280200

Mattick JS; Amaral PP; Dinger ME; Mercer TR; Mehler MF, 2009, 'RNA regulation of epigenetic processes', BioEssays, 31, pp. 51 - 59, http://dx.doi.org/10.1002/bies.080099

Dinger ME; Pang KC; Mercer TR; Crowe ML; Grimmond SM; Mattick JS, 2009, 'NRED: A database of long noncoding RNA expression', Nucleic Acids Research, 37, http://dx.doi.org/10.1093/nar/gkn617

Mattick JS, 2009, 'Deconstructing the dogma: A new view of the evolution and genetic programming of complex organisms', Annals of the New York Academy of Sciences, 1178, pp. 29 - 46, http://dx.doi.org/10.1111/j.1749-6632.2009.04991.x

Mercer TR; Dinger ME; Mariani J; Kosik KS; Mehler MF; Mattick JS, 2008, 'Noncoding RNAs in long-term memory formation', Neuroscientist, 14, pp. 434 - 445, http://dx.doi.org/10.1177/1073858408319187

Korbie DJ; Mattick JS, 2008, 'Touchdown PCR for increased specificity and sensitivity in PCR amplification', Nature Protocols, 3, pp. 1452 - 1456, http://dx.doi.org/10.1038/nprot.2008.133

Nahkuri S; Taft RJ; Korbie DJ; Mattick JS, 2008, 'Molecular Evolution of the HBII-52 snoRNA Cluster', Journal of Molecular Biology, 381, pp. 810 - 815, http://dx.doi.org/10.1016/j.jmb.2008.06.057

Dinger ME; Amara 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; Mattick JS, 2008, 'Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation', Genome Research, 18, pp. 1433 - 1445, http://dx.doi.org/10.1101/gr.078378.108

Amaral PP; Mattick JS, 2008, 'Noncoding RNA in development', Mammalian Genome, 19, pp. 454 - 492, http://dx.doi.org/10.1007/s00335-008-9136-7

Keith JM; Adams P; Stephen S; Mattick JS, 2008, 'Delineating slowly and rapidly evolving fractions of the Drosophila genome', Journal of Computational Biology, 15, pp. 407 - 430, http://dx.doi.org/10.1089/cmb.2007.0173

Mattick JS; Mehler MF, 2008, 'RNA editing, DNA recoding and the evolution of human cognition', Trends in Neurosciences, 31, pp. 227 - 233, http://dx.doi.org/10.1016/j.tins.2008.02.003

Mattick JS; Croft LJ; Pheasant M; Mercer TR; Dinger ME, 2008, 'The mammalian genome as an RNA machine', FASEB JOURNAL, 22, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000208467805697&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Amaral PP; Dinger ME; Mercer TR; Mattick JS, 2008, 'The eukaryotic genome as an RNA machine', Science, 319, pp. 1787 - 1789, http://dx.doi.org/10.1126/science.1155472

Dinger ME; Mercer TR; Mattick JS, 2008, 'RNAs as extracellular signaling molecules', Journal of Molecular Endocrinology, 40, pp. 151 - 159, http://dx.doi.org/10.1677/JME-07-0160

Stephen S; Pheasant M; Makunin IV; Mattick JS, 2008, 'Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock', Molecular Biology and Evolution, 25, pp. 402 - 408, http://dx.doi.org/10.1093/molbev/msm268

Mercer TR; Dinger ME; Sunkin SM; Mehler MF; Mattick JS, 2008, 'Specific expression of long noncoding RNAs in the mouse brain', Proceedings of the National Academy of Sciences of the United States of America, 105, pp. 716 - 721, http://dx.doi.org/10.1073/pnas.0706729105

Dinger ME; Pang KC; Mercer TR; Mattick JS, 2008, 'Differentiating protein-coding and noncoding RNA: Challenges and ambiguities', PLoS Computational Biology, 4, http://dx.doi.org/10.1371/journal.pcbi.1000176

Simons C; Makunin IV; Pheasant M; Mattick JS, 2007, 'Maintenance of transposon-free regions throughout vertebrate evolution', BMC Genomics, 8, http://dx.doi.org/10.1186/1471-2164-8-470

Frith MC; Carninci P; Kai C; Kawai J; Bailey TL; Hayashizaki Y; Mattick JS, 2007, 'Splicing bypasses 3′ end formation signals to allow complex gene architectures', Gene, 403, pp. 188 - 193, http://dx.doi.org/10.1016/j.gene.2007.08.012

Makunin IV; Pheasant M; Simons C; Mattick JS, 2007, 'Orthologous microRNA genes are located in cancer-associated genomic regions in human and mouse', PLoS ONE, 2, http://dx.doi.org/10.1371/journal.pone.0001133

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