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Items: 20

1.

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Pandolfini L, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, Kouzarides T.

Genome Biol. 2018 Mar 15;19(1):32. doi: 10.1186/s13059-018-1405-5.

2.

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation.

Li MA, Amaral PP, Cheung P, Bergmann JH, Kinoshita M, Kalkan T, Ralser M, Robson S, von Meyenn F, Paramor M, Yang F, Chen C, Nichols J, Spector DL, Kouzarides T, He L, Smith A.

Elife. 2017 Aug 18;6. pii: e23468. doi: 10.7554/eLife.23468.

3.

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.

4.

Re-place your BETs: the dynamics of super enhancers.

Amaral PP, Bannister AJ.

Mol Cell. 2014 Oct 23;56(2):187-189. doi: 10.1016/j.molcel.2014.10.008. No abstract available.

5.

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells.

Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T.

Genome Biol. 2013;14(9):R98.

6.

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
7.

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.

Bioinformatics. 2012 Dec 1;28(23):3042-50. doi: 10.1093/bioinformatics/bts582. Epub 2012 Oct 7.

PMID:
23044541
8.

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.

PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. doi: 10.1371/journal.pbio.1000625. Epub 2011 Jul 12. No abstract available.

9.

lncRNAdb: a reference database for long noncoding RNAs.

Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS.

Nucleic Acids Res. 2011 Jan;39(Database issue):D146-51. doi: 10.1093/nar/gkq1138. Epub 2010 Nov 25.

10.

Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.

Dinger ME, Amaral PP, Mercer TR, Mattick JS.

Brief Funct Genomic Proteomic. 2009 Nov;8(6):407-23. doi: 10.1093/bfgp/elp038. Epub 2009 Sep 21.

PMID:
19770204
11.

Complex architecture and regulated expression of the Sox2ot locus during vertebrate development.

Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS.

RNA. 2009 Nov;15(11):2013-27. doi: 10.1261/rna.1705309. Epub 2009 Sep 18.

12.

RNA regulation of epigenetic processes.

Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF.

Bioessays. 2009 Jan;31(1):51-9. doi: 10.1002/bies.080099. Review.

PMID:
19154003
13.

MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles.

Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL.

Genome Res. 2009 Mar;19(3):347-59. doi: 10.1101/gr.087775.108. Epub 2008 Dec 22.

14.

Noncoding RNA in development.

Amaral PP, Mattick JS.

Mamm Genome. 2008 Aug;19(7-8):454-92. doi: 10.1007/s00335-008-9136-7. Epub 2008 Oct 7. Review.

PMID:
18839252
15.

Bird mixed-flocks and nuclear species in a tecoma savanna in the Pantanal.

Amaral PP, Ragusa-Netto J.

Braz J Biol. 2008 Aug;68(3):511-8.

16.

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.

Genome Res. 2008 Sep;18(9):1433-45. doi: 10.1101/gr.078378.108. Epub 2008 Jun 18.

17.

Protein requirements for Blue-fronted Amazon (Amazona aestiva) growth.

Carciofi AC, Sanfilippo LF, de-Oliveira LD, do Amaral PP, Prada F.

J Anim Physiol Anim Nutr (Berl). 2008 Jun;92(3):363-8. doi: 10.1111/j.1439-0396.2007.00800.x.

PMID:
18477318
18.

The eukaryotic genome as an RNA machine.

Amaral PP, Dinger ME, Mercer TR, Mattick JS.

Science. 2008 Mar 28;319(5871):1787-9. doi: 10.1126/science.1155472.

PMID:
18369136
19.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira YB, El-Jundi TA, da Silva AM, Reis EM, Verjovski-Almeida S.

Genome Biol. 2007;8(3):R43.

20.

Androgen responsive intronic non-coding RNAs.

Louro R, Nakaya HI, Amaral PP, Festa F, Sogayar MC, da Silva AM, Verjovski-Almeida S, Reis EM.

BMC Biol. 2007 Jan 30;5:4.

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