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The eukaryotic genome as an RNA machine.
Amaral PP, Dinger ME, Mercer TR, Mattick JS. Amaral PP, et al. Science. 2008 Mar 28;319(5871):1787-9. doi: 10.1126/science.1155472. Science. 2008. PMID: 18369136
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation.
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. Dinger ME, et al. Among authors: amaral pp. Genome Res. 2008 Sep;18(9):1433-45. doi: 10.1101/gr.078378.108. Epub 2008 Jun 18. Genome Res. 2008. PMID: 18562676 Free PMC article.
Noncoding RNA in development.
Amaral PP, Mattick JS. Amaral PP, et al. Mamm Genome. 2008 Aug;19(7-8):454-92. doi: 10.1007/s00335-008-9136-7. Epub 2008 Oct 7. Mamm Genome. 2008. PMID: 18839252 Review.
RNA regulation of epigenetic processes.
Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF. Mattick JS, et al. Among authors: amaral pp. Bioessays. 2009 Jan;31(1):51-9. doi: 10.1002/bies.080099. Bioessays. 2009. PMID: 19154003 Review.
lncRNAdb: a reference database for long noncoding RNAs.
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. Amaral PP, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D146-51. doi: 10.1093/nar/gkq1138. Epub 2010 Nov 25. Nucleic Acids Res. 2011. PMID: 21112873 Free PMC article.
The reality of pervasive transcription.
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. Clark MB, et al. Among authors: amaral pp. PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. doi: 10.1371/journal.pbio.1000625. Epub 2011 Jul 12. PLoS Biol. 2011. PMID: 21765801 Free PMC article.
Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.
Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS. Gascoigne DK, et al. Among authors: amaral pp. Bioinformatics. 2012 Dec 1;28(23):3042-50. doi: 10.1093/bioinformatics/bts582. Epub 2012 Oct 7. Bioinformatics. 2012. PMID: 23044541
27 results