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Items: 1 to 20 of 42


A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.

Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY.

Nature. 2011 Apr 7;472(7341):120-4. doi: 10.1038/nature09819. Epub 2011 Mar 20.


Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.

Heo JB, Sung S.

Science. 2011 Jan 7;331(6013):76-9. doi: 10.1126/science.1197349. Epub 2010 Dec 2.


The evolution of gene regulation, the RNA universe, and the vexed questions of artefact and noise.

Robertson M.

BMC Biol. 2010 Jul 16;8:97. doi: 10.1186/1741-7007-8-97. No abstract available.


Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

Xu AG, He L, Li Z, Xu Y, Li M, Fu X, Yan Z, Yuan Y, Menzel C, Li N, Somel M, Hu H, Chen W, Pääbo S, Khaitovich P.

PLoS Comput Biol. 2010 Jul 1;6:e1000843. doi: 10.1371/journal.pcbi.1000843.


Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.

Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M.

BMC Genomics. 2010 Jun 17;11:383. doi: 10.1186/1471-2164-11-383.


Dark matter transcripts: sound and fury, signifying nothing?

Robinson R.

PLoS Biol. 2010 May 18;8(5):e1000370. doi: 10.1371/journal.pbio.1000370. No abstract available.


Most "dark matter" transcripts are associated with known genes.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR.

PLoS Biol. 2010 May 18;8(5):e1000371. doi: 10.1371/journal.pbio.1000371.


Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.


Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A.

Nat Biotechnol. 2010 May;28(5):503-10. doi: 10.1038/nbt.1633. Epub 2010 May 2. Erratum in: Nat Biotechnol. 2010 Jul;28(7):756.


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.


Pervasive transcription constitutes a new level of eukaryotic genome regulation.

Berretta J, Morillon A.

EMBO Rep. 2009 Sep;10(9):973-82. doi: 10.1038/embor.2009.181. Epub 2009 Aug 14. Review.


Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.

Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, Raymond CK.

Nat Methods. 2009 Sep;6(9):647-9. doi: 10.1038/nmeth.1360. Epub 2009 Aug 9.


Conserved introns reveal novel transcripts in Drosophila melanogaster.

Hiller M, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF.

Genome Res. 2009 Jul;19(7):1289-300. doi: 10.1101/gr.090050.108. Epub 2009 May 20.


TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.


Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain.

Azevedo FA, Carvalho LR, Grinberg LT, Farfel JM, Ferretti RE, Leite RE, Jacob Filho W, Lent R, Herculano-Houzel S.

J Comp Neurol. 2009 Apr 10;513(5):532-41. doi: 10.1002/cne.21974.


Long non-coding RNAs: insights into functions.

Mercer TR, Dinger ME, Mattick JS.

Nat Rev Genet. 2009 Mar;10(3):155-9. doi: 10.1038/nrg2521. Review.


Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.

Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project.

Nature. 2009 Feb 19;457(7232):1028-32. doi: 10.1038/nature07759. Epub 2009 Jan 25.


A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster.

Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M.

Mol Cell. 2008 Dec 5;32(5):685-95. doi: 10.1016/j.molcel.2008.09.027.


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.


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.

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