Publications

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Mattick Lab publications on noncoding RNAs and transcriptomics

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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. Nat Protoc. 9: 989-1009

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 Oct 29. doi:pii: S2211-1247(13)00559-7

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. doi: 10.4161/cc.25134

Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen L, Mattick JS, Stamatoyannopoulos JA (2013). DNaseI-hypersensitive exons co-localize with promoters and distal regulatory elements. Nat Genet. 45: 852-9

Smith MA, Gesell T, Stadler PF, Mattick JS (2013). Widespread purifying selection on RNA structure in mammals. Nucl. Acids Res. 2013 41 (17): 8220-8236. doi: 10.1093/nar/gkt596

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

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

Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, 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 28:3042-50

Buske FA, Bauer DC, Mattick JS, Bailey TL (2012) Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res. May 1. [Epub ahead of print]

Clark MB, 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 Res. 22: 885-898.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL (2012). Targeted RNA sequencing reveals the deep complexity of the human transcriptome Nat Biotech. 30: 99–104.

Mattick JS, Clark MB (2011) RNA lights up Nat Biotech. 29: 883–884.

Mercer TR, Neph S, Dinger ME, Crawford J, Smith MS, Shearwood A-MJ, Rackham O, Haugen E, Stamatoyannopoulos JA, Filopovska A, and Mattick JS (2011). The human mitochondrial transcriptome. Cell 146: 645-658.

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

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 Res 71: 3852-3862.

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: 878-891.

Clark MB, Mattick JS (2011) Long noncoding RNAs in cell biology. Semin Cell Dev Biol. 22: 366–376.

Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (2011). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 39 (suppl 1): D146-D151.

Mercer TR, Wilhelm D, Dinger ME, Solda G, Korbie DJ, Glazov EA, Truong V, Schwenke M, Simons C, Matthaei KI, Saint R, Koopman P, Mattick JS (2010). Expression of distinct RNAs from 3’ untranslated regions. Nucleic Acids Res. Published online 12 November 2010.

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 Res. Published online 2 November 2010 .

Fernandez-Valverde SL, Taft RJ, Mattick JS (2010). Dynamic isomiR regulation in Drosophila development. RNA 16: 1881-1888.

Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ, Rasko JE, Rokhsar DS, Degnan BM, Mattick JS (2010). Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol 17: 1030-1034.

Jung CH, Makunin IV, Mattick JS (2010). Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs. Genomics 96: 154-166.

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: 548-552.

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. Mol Genet Genom 284: 1-9.

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: 1156-66.

Mercer TR, Qureshi IA, Goken 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: 14.

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: 77.

de Hoon MJ, 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 Res 20: 257-264.

Mattick JS, Taft RJ, Faulkner GJ (2010). A global view of genomic information--moving beyond the gene and the master regulator. Trends Genet 26: 21-8.

Taft RJ, Pang KC, Mercer TR, Dinger ME, Mattick JS (2010). Non-coding RNAs: regulators of disease. J Pathol 220: 126-39.

Mattick JS (2009). Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms. Ann N Y Acad Sci. 1178: 29-46.

Nahkuri S, Taft RJ, Mattick JS (2009). Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle 8: 3420-4.

Dinger ME, Amaral PP, Mercer TR, Mattick JS (2009). Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomic Proteomic. 8: 407-23 Free access preprint (15 June 2009).

Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AM, Mattick JS (2009) Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA. 15: 2013-27.

Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chan W, Mattick JS (2009). Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol. 182: 7738-7748.

Taft RJ, Kaplan CD, Simons C, Mattick JS (2009). Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 8: 2332-8.

Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS (2009). Small RNAs derived from snoRNAs. RNA. 8: 2332-8

Mattick JS (2009). The genetic signatures of noncoding RNAs. PLoS Genet. 5: e1000459.

Guffanti A, Iacono M, Pelucchi P, Kim N, Solda G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Rossi 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: 163

Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, 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. Nat Genet. Epub Apr 19.

The FANTOM Consortium, Suzuki H et al. (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. Epub Apr 19.

Mercer TR, Dinger ME, Mattick JS (2009). Long noncoding RNAs: insights into function. Nat Rev Genet. 10: 155-159.

Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009). RNA regulation of epigenetic processes. Bioessays. 31: 51-59.

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 Res 19: 347-359.

Webster RJ, Giles KM, Price KJ, Zhang PM, Mattick JS and Leedman PJ (2009) Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7. J Biol Chem 284: 5731-5741.

Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS (2009). NRED: a database of long noncoding RNA expression. Nucleic Acid Res 37: D122-126.

Mercer TR, Dinger ME, Mariani J, Kosik KS, Mehler MF, Mattick JS (2008). Noncoding RNAs in long-term memory formation. Neuroscientist. 14: 434-445.

Amaral PP, Mattick JS (2008). Noncoding RNA in development. Mamm Genome 19: 454-492.

Korbie DJ, Mattick JS (2008). Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc 3: 1452-1456.

Dinger ME, Pang KC, Mercer TR, Mattick JS (2008). Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comp Biol 4: e1000176.

Nahkuri S, Taft RJ, Korbie DJ, Mattick JS (2008). Molecular evolution of the HBII-52 snoRNA cluster. J Mol Biol 381: 810-815.

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, Mattick JS (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445.

Keith JM, Adams P, Stephen S, Mattick JS (2008). Delineating slowly and rapidly evolving fractions of the Drosophila genome. J Comput Biol.

Mattick JS, Mehler MF (2008). RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci 31: 227-233.

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

Dinger ME, Mercer TR, Mattick JS (2008). RNAs as extracellular signaling molecules. J Mol Endocrinol 40: 151-159.

Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008). Specific expression of long noncoding RNAs in the adult mouse brain. Proc Natl Acad Sci USA 105: 716-721.

Simons C, Makunin IV, Pheasant M, Mattick JS (2007). Maintenance of transposon-free regions throughout vertebrate evolution. BMC Genomics 8: 470.

Stephen S, Pheasant M, Makunin IV, Mattick JS (2007). Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol Biol Evol 25: 402-408.

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: e1133.

Pheasant M, Mattick JS (2007). Raising the estimate of functional human sequences. Genome Res 17: 1245-1253.

Mehler MF, Mattick JS (2007). Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev 87: 799-823.

ENCODE consortium (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.

Mattick, JS (2007). A new paradigm for developmental biology. J Exp Biol 210: 1526-1547.

Pang, KC, Stephen, S, Dinger, ME, Engstrom, PG, Lenhard, B, Mattick, JS (2007). RNAdb 2.0--an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 35: D178-182.

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

Mehler, MF, Mattick, JS (2006). Non-coding RNAs in the nervous system. J Physiol 575: 333-341.

Frith, MC, Bailey, TL, Kasukawa, T, Mignone, F, Kummerfeld, SK, Madera, M, Sunkara, S, Furuno, M, Bult, CJ, Quackenbush, J, et al. (2006). Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol 3.

Furuno, M, Pang, KC, Ninomiya, N, Fukuda, S, Frith, MC, Bult, C, Kai, C, Kawai, J, Carninci, P, Hayashizaki, Y, et al. (2006). Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet 2: e37.

Glazov, EA, Pheasant, M, Nahkuri, S, Mattick, JS (2006). Evidence for control of splicing by alternative RNA secondary structures in Dipteran homothorax pre-mRNA. RNA Biol 3.

Kenzelmann, M, Rippe, K, Mattick, JS (2006). RNA: Networks & Imaging. Mol Syst Biol 2: 44.

Simons, C, Pheasant, M, Makunin, IV, Mattick, JS (2006). Transposon-free regions in mammalian genomes. Genome Res 16: 164-172.

Pang, KC, Frith, MC, Mattick, JS (2006). Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22: 1-5.

Ravasi, T, Suzuki, H, Pang, KC, Katayama, S, Furuno, M, Okunishi, R, Fukuda, S, Ru, K, Frith, MC, Gongora, MM, et al. (2006). Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 16: 11-19.

Stanley, SM, Bailey, TL, Mattick, JS (2006). GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinformatics 7: 94.

Mattick, JS, Makunin, IV (2006). Non-coding RNA. Hum Mol Genet 15: R17-R29.

Mattick, JS (2005). The functional genomics of noncoding RNA. Science 309: 1527-1528.

Carninci, P, Kasukawa, T, Katayama, S, Gough, J, Frith, MC, Maeda, N, Oyama, R, Ravasi, T, Lenhard, B, Wells, C, et al. (2005). The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.

Katayama, S, Tomaru, Y, Kasukawa, T, Waki, K, Nakanishi, M, Nakamura, M, Nishida, H, Yap, CC, Suzuki, M, Kawai, J, Suzuki, H, Carninci, P, Hayashizaki, Y, Wells, C, Frith, M, Ravasi, T, Pang, KC, Hallinan, J, Mattick, JS, et al. Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.

Frith, MC, Pheasant, M, Mattick, JS (2005). The amazing complexity of the human transcriptome. Eur J Hum Genet 13: 894-897.

Gagen, MJ, Mattick, JS (2005). Accelerating, hyperaccelerating, and decelerating networks. Phys Rev E Stat Nonlin Soft Matter Phys 72: 016123.

Mattick, JS, Gagen, MJ (2005). Mathematics/computation. Accelerating networks. Science 307: 856-858.

Mattick, JS, Makunin, IV (2005). Small regulatory RNAs in mammals. Hum Mol Genet 14 Spec No 1: R121-R132.

Pang, KC, Stephen, S, Engstrom, PG, Tajul-Arifin, K, Chen, W, Wahlestedt, C, Lenhard, B, Hayashizaki, Y, Mattick, JS (2005). RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res 33: D125-130.

Bejerano, G, Pheasant, M, Makunin, I, Stephen, S, Kent, WJ, Mattick, JS, Haussler, D (2004). Ultraconserved elements in the human genome. Science 304: 1321-1325.

Mattick, JS (2004). The hidden genetic program of complex organisms. Sci Am 291: 60-67.

Mattick, JS (2004). The regulatory architecture of the human genome. Asia Pac J Clin Nutr 13: S14.

Mattick, JS (2004). RNA regulation: a new genetics? Nat Rev Genet 5: 316-323.

Mattick, JS (2003). Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25: 930-939.

Mattick, JS (2003). The human genome and the future of medicine. Med J Aust 179: 212-216.

Mattick, JS (2001). Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2: 986-991.

Mattick, JS, Gagen, MJ (2001). The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 18: 1611-1630.

Mattick, JS (1994). Introns: evolution and function. Curr Opin Genet Dev 4: 823-831.

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