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Results: 1 to 20 of 114

1.

Noncoder: a web interface for exon array-based detection of long non-coding RNAs.

Gellert P, Ponomareva Y, Braun T, Uchida S.

Nucleic Acids Res. 2013 Jan 7;41(1):e20. doi: 10.1093/nar/gks877. Epub 2012 Sep 24.

PMID:
23012263
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

ncFANs: a web server for functional annotation of long non-coding RNAs.

Liao Q, Xiao H, Bu D, Xie C, Miao R, Luo H, Zhao G, Yu K, Zhao H, Skogerbø G, Chen R, Wu Z, Liu C, Zhao Y.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W118-24. doi: 10.1093/nar/gkr432.

PMID:
21715382
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Exon Array Analyzer: a web interface for Affymetrix exon array analysis.

Gellert P, Uchida S, Braun T.

Bioinformatics. 2009 Dec 15;25(24):3323-4. doi: 10.1093/bioinformatics/btp577. Epub 2009 Oct 6.

PMID:
19808879
[PubMed - indexed for MEDLINE]
Free Article
4.

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
5.

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
6.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Yates T, Okoniewski MJ, Miller CJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D780-6. Epub 2007 Oct 11.

PMID:
17932061
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

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
9.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060. Epub 2012 Nov 17.

PMID:
23161675
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments.

Consiglio A, Carella M, De Caro G, Delle Foglie G, Giovannelli C, Grillo G, Ianigro M, Licciulli F, Palumbo O, Piepoli A, Ranieri E, Liuni S.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S21. doi: 10.1186/1471-2105-13-S4-S21.

PMID:
22536968
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

MADS+: discovery of differential splicing events from Affymetrix exon junction array data.

Shen S, Warzecha CC, Carstens RP, Xing Y.

Bioinformatics. 2010 Jan 15;26(2):268-9. doi: 10.1093/bioinformatics/btp643. Epub 2009 Nov 17.

PMID:
19933160
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs.

Hassan MA, Melo MB, Haas B, Jensen KD, Saeij JP.

BMC Genomics. 2012 Dec 12;13:696. doi: 10.1186/1471-2164-13-696.

PMID:
23231500
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Overestimation of alternative splicing caused by variable probe characteristics in exon arrays.

Gaidatzis D, Jacobeit K, Oakeley EJ, Stadler MB.

Nucleic Acids Res. 2009 Sep;37(16):e107. doi: 10.1093/nar/gkp508. Epub 2009 Jun 15.

PMID:
19528075
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

ExonMiner: Web service for analysis of GeneChip Exon array data.

Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S.

BMC Bioinformatics. 2008 Nov 26;9:494. doi: 10.1186/1471-2105-9-494.

PMID:
19036125
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Analysis of long non-coding RNA expression profiles in gastric cancer.

Cao WJ, Wu HL, He BS, Zhang YS, Zhang ZY.

World J Gastroenterol. 2013 Jun 21;19(23):3658-64. doi: 10.3748/wjg.v19.i23.3658.

PMID:
23801869
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs.

Risueño A, Fontanillo C, Dinger ME, De Las Rivas J.

BMC Bioinformatics. 2010 Apr 29;11:221. doi: 10.1186/1471-2105-11-221.

PMID:
20429936
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing.

Li T, Wang S, Wu R, Zhou X, Zhu D, Zhang Y.

Genomics. 2012 May;99(5):292-8. doi: 10.1016/j.ygeno.2012.02.003. Epub 2012 Feb 20.

PMID:
22374175
[PubMed - indexed for MEDLINE]
Free Article
18.

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
19.

LncRNAs expression signatures of renal clear cell carcinoma revealed by microarray.

Yu G, Yao W, Wang J, Ma X, Xiao W, Li H, Xia D, Yang Y, Deng K, Xiao H, Wang B, Guo X, Guan W, Hu Z, Bai Y, Xu H, Liu J, Zhang X, Ye Z.

PLoS One. 2012;7(8):e42377. doi: 10.1371/journal.pone.0042377. Epub 2012 Aug 6.

PMID:
22879955
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF.

Bioinformatics. 2011 Jul 15;27(14):1894-900. doi: 10.1093/bioinformatics/btr314. Epub 2011 May 26.

PMID:
21622663
[PubMed - indexed for MEDLINE]
Free Article

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