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Results: 1 to 20 of 148

1.

Long noncoding RNAs are rarely translated in two human cell lines.

Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L.

Genome Res. 2012 Sep;22(9):1646-57. doi: 10.1101/gr.134767.111.

PMID:
22955977
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R.

Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111.

PMID:
22955988
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs.

Jalali S, Jayaraj GG, Scaria V.

Biol Direct. 2012 Aug 7;7:25. doi: 10.1186/1745-6150-7-25.

PMID:
22871084
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

PMID:
22955987
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions.

Khatun J, Yu Y, Wrobel JA, Risk BA, Gunawardena HP, Secrest A, Spitzer WJ, Xie L, Wang L, Chen X, Giddings MC.

BMC Genomics. 2013 Feb 28;14:141. doi: 10.1186/1471-2164-14-141.

PMID:
23448259
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Long noncoding RNAs in C. elegans.

Nam JW, Bartel DP.

Genome Res. 2012 Dec;22(12):2529-40. doi: 10.1101/gr.140475.112. Epub 2012 Jun 15.

PMID:
22707570
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs.

Niazi F, Valadkhan S.

RNA. 2012 Apr;18(4):825-43. doi: 10.1261/rna.029520.111. Epub 2012 Feb 23.

PMID:
22361292
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

LNCipedia: a database for annotated human lncRNA transcript sequences and structures.

Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D246-51. doi: 10.1093/nar/gks915. Epub 2012 Oct 5.

PMID:
23042674
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Genome-wide analysis of long noncoding RNA stability.

Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME, Mattick JS.

Genome Res. 2012 May;22(5):885-98. doi: 10.1101/gr.131037.111. Epub 2012 Mar 9.

PMID:
22406755
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.

Chen G, Yin K, Shi L, Fang Y, Qi Y, Li P, Luo J, He B, Liu M, Shi T.

PLoS One. 2011;6(11):e28318. doi: 10.1371/journal.pone.0028318. Epub 2011 Nov 30.

PMID:
22140575
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genome-wide computational identification and manual annotation of human long noncoding RNA genes.

Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L.

RNA. 2010 Aug;16(8):1478-87. doi: 10.1261/rna.1951310. Epub 2010 Jun 29.

PMID:
20587619
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Systematic transcriptome wide analysis of lncRNA-miRNA interactions.

Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V.

PLoS One. 2013;8(2):e53823. doi: 10.1371/journal.pone.0053823. Epub 2013 Feb 6.

PMID:
23405074
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Activity-dependent human brain coding/noncoding gene regulatory networks.

Lipovich L, Dachet F, Cai J, Bagla S, Balan K, Jia H, Loeb JA.

Genetics. 2012 Nov;192(3):1133-48. doi: 10.1534/genetics.112.145128. Epub 2012 Sep 7.

PMID:
22960213
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Diversity of translation start sites may define increased complexity of the human short ORFeome.

Oyama M, Kozuka-Hata H, Suzuki Y, Semba K, Yamamoto T, Sugano S.

Mol Cell Proteomics. 2007 Jun;6(6):1000-6. Epub 2007 Feb 21.

PMID:
17317662
[PubMed - indexed for MEDLINE]
Free Article
15.

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs.

Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, Jain S, Sati S, Sengupta S, Sachidanandan C, Raghava GP, Sivasubbu S, Scaria V.

Database (Oxford). 2013 Jul 11;2013:bat034. doi: 10.1093/database/bat034. Print 2013.

PMID:
23846593
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.

Sun L, Zhang Z, Bailey TL, Perkins AC, Tallack MR, Xu Z, Liu H.

BMC Bioinformatics. 2012 Dec 13;13:331. doi: 10.1186/1471-2105-13-331.

PMID:
23237380
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Aberrant expression of long noncoding RNAs in cervical intraepithelial neoplasia.

Gibb EA, Becker-Santos DD, Enfield KS, Guillaud M, Niekerk Dv, Matisic JP, Macaulay CE, Lam WL.

Int J Gynecol Cancer. 2012 Nov;22(9):1557-63. doi: 10.1097/IGC.0b013e318272f2c9.

PMID:
23095774
[PubMed - indexed for MEDLINE]
18.

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
[PubMed - indexed for MEDLINE]
Free Article
19.

Long non-coding RNAs: a new frontier in the study of human diseases.

Shi X, Sun M, Liu H, Yao Y, Song Y.

Cancer Lett. 2013 Oct 10;339(2):159-66. doi: 10.1016/j.canlet.2013.06.013. Epub 2013 Jun 18. Review.

PMID:
23791884
[PubMed - indexed for MEDLINE]
20.

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails.

Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA.

Genes Dev. 2012 Nov 1;26(21):2392-407. doi: 10.1101/gad.204438.112. Epub 2012 Oct 16.

PMID:
23073843
[PubMed - indexed for MEDLINE]
Free PMC Article

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