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Items: 1 to 20 of 161

1.

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.

Ragan C, Mowry BJ, Bauer DC.

Nucleic Acids Res. 2012 Sep;40(16):7633-43. doi: 10.1093/nar/gks505. Epub 2012 Jun 16.

2.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

3.

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data.

Jung CH, Hansen MA, Makunin IV, Korbie DJ, Mattick JS.

BMC Genomics. 2010 Feb 1;11:77. doi: 10.1186/1471-2164-11-77.

4.

Identification and classification of small RNAs in transcriptome sequence data.

Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S.

Pac Symp Biocomput. 2010:80-7.

5.

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.

Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W112-7. doi: 10.1093/nar/gkr357. Epub 2011 May 27.

6.

ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins.

Tempel S, Pollet N, Tahi F.

BMC Bioinformatics. 2012 Sep 25;13:246. doi: 10.1186/1471-2105-13-246.

7.

Novel insight into the non-coding repertoire through deep sequencing analysis.

Isakov O, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N.

Nucleic Acids Res. 2012 Jun;40(11):e86. doi: 10.1093/nar/gks228. Epub 2012 Mar 9.

8.

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.

Videm P, Rose D, Costa F, Backofen R.

Bioinformatics. 2014 Jun 15;30(12):i274-82. doi: 10.1093/bioinformatics/btu270.

9.

DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

Yang JH, Qu LH.

Methods Mol Biol. 2012;822:233-48. doi: 10.1007/978-1-61779-427-8_16.

PMID:
22144203
10.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

Luo GZ, Yang W, Ma YK, Wang XJ.

Bioinformatics. 2014 Feb 1;30(3):434-6. doi: 10.1093/bioinformatics/btt678. Epub 2013 Dec 3.

PMID:
24300438
11.

PsRobot: a web-based plant small RNA meta-analysis toolbox.

Wu HJ, Ma YK, Chen T, Wang M, Wang XJ.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W22-8. doi: 10.1093/nar/gks554. Epub 2012 Jun 12.

12.

Deep sequencing analysis of small non-coding RNAs reveals the diversity of microRNAs and piRNAs in the human epididymis.

Li Y, Wang HY, Wan FC, Liu FJ, Liu J, Zhang N, Jin SH, Li JY.

Gene. 2012 Apr 15;497(2):330-5. doi: 10.1016/j.gene.2012.01.038. Epub 2012 Jan 31.

PMID:
22313525
13.

CPSS: a computational platform for the analysis of small RNA deep sequencing data.

Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X, Cooke HJ, Xue Y, Shi Q.

Bioinformatics. 2012 Jul 15;28(14):1925-7. doi: 10.1093/bioinformatics/bts282. Epub 2012 May 9.

PMID:
22576177
14.

FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.

Hoogstrate Y, Jenster G, Martens-Uzunova ES.

Bioinformatics. 2015 Mar 1;31(5):665-73. doi: 10.1093/bioinformatics/btu696. Epub 2014 Oct 22.

PMID:
25338717
15.

psRNATarget: a plant small RNA target analysis server.

Dai X, Zhao PX.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W155-9. doi: 10.1093/nar/gkr319. Epub 2011 May 27.

16.

Classification of ncRNAs using position and size information in deep sequencing data.

Erhard F, Zimmer R.

Bioinformatics. 2010 Sep 15;26(18):i426-32. doi: 10.1093/bioinformatics/btq363.

17.

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.

Pantano L, Estivill X, Martí E.

Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.

PMID:
21976421
18.

RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs.

Michaeli S, Doniger T, Gupta SK, Wurtzel O, Romano M, Visnovezky D, Sorek R, Unger R, Ullu E.

Nucleic Acids Res. 2012 Feb;40(3):1282-98. doi: 10.1093/nar/gkr786. Epub 2011 Oct 5.

19.

Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells.

Guduric-Fuchs J, O'Connor A, Cullen A, Harwood L, Medina RJ, O'Neill CL, Stitt AW, Curtis TM, Simpson DA.

J Cell Biochem. 2012 Jun;113(6):2098-111. doi: 10.1002/jcb.24084.

20.

Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs.

Ryvkin P, Leung YY, Ungar LH, Gregory BD, Wang LS.

Methods. 2014 May 1;67(1):28-35. doi: 10.1016/j.ymeth.2013.10.002. Epub 2013 Oct 18.

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