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Items: 1 to 20 of 35

1.

miRSeqNovel: an R based workflow for analyzing miRNA sequencing data.

Qian K, Auvinen E, Greco D, Auvinen P.

Mol Cell Probes. 2012 Oct;26(5):208-11. doi: 10.1016/j.mcp.2012.05.002. Epub 2012 May 17.

PMID:
22609373
2.

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments.

Wen M, Shen Y, Shi S, Tang T.

BMC Bioinformatics. 2012 Jun 21;13:140. doi: 10.1186/1471-2105-13-140.

3.

Discovering microRNAs from deep sequencing data using miRDeep.

Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N.

Nat Biotechnol. 2008 Apr;26(4):407-15. doi: 10.1038/nbt1394.

PMID:
18392026
4.

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs.

Xie F, Xiao P, Chen D, Xu L, Zhang B.

Plant Mol Biol. 2012 Jan 31. [Epub ahead of print]

PMID:
22290409
5.

SplamiR--prediction of spliced miRNAs in plants.

Thieme CJ, Gramzow L, Lobbes D, Theissen G.

Bioinformatics. 2011 May 1;27(9):1215-23. doi: 10.1093/bioinformatics/btr132. Epub 2011 Mar 17.

PMID:
21421552
6.

miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.

Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS.

BMC Bioinformatics. 2009 Oct 12;10:328. doi: 10.1186/1471-2105-10-328.

7.

miRNA data analysis: next-gen sequencing.

Gunaratne PH, Coarfa C, Soibam B, Tandon A.

Methods Mol Biol. 2012;822:273-88. doi: 10.1007/978-1-61779-427-8_19.

PMID:
22144206
8.

Computational identification of novel microRNAs and targets in Brassica napus.

Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM.

FEBS Lett. 2007 Apr 3;581(7):1464-74. Epub 2007 Mar 8.

9.

mirExplorer: detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features.

Guan DG, Liao JY, Qu ZH, Zhang Y, Qu LH.

RNA Biol. 2011 Sep-Oct;8(5):922-34. doi: 10.4161/rna.8.5.16026. Epub 2011 Sep 1.

PMID:
21881406
10.

A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing.

Guo L, Liang T, Lu Z.

Biosystems. 2011 May-Jun;104(2-3):87-93. doi: 10.1016/j.biosystems.2011.01.004. Epub 2011 Jan 13.

PMID:
21237247
11.

wapRNA: a web-based application for the processing of RNA sequences.

Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C, Li R, Ling Y, Wu J, Song S, Hu S.

Bioinformatics. 2011 Nov 1;27(21):3076-7. doi: 10.1093/bioinformatics/btr504. Epub 2011 Sep 6.

PMID:
21896507
12.

SoMART: a web server for plant miRNA, tasiRNA and target gene analysis.

Li F, Orban R, Baker B.

Plant J. 2012 Jun;70(5):891-901. doi: 10.1111/j.1365-313X.2012.04922.x. Epub 2012 Mar 8.

13.

CID-miRNA: a web server for prediction of novel miRNA precursors in human genome.

Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, Srinivasan A, Bhattacharya A.

Biochem Biophys Res Commun. 2008 Aug 8;372(4):831-4. doi: 10.1016/j.bbrc.2008.05.134. Epub 2008 Jun 2.

PMID:
18522801
14.

Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.

Yang X, Zhang H, Li L.

Plant J. 2012 May;70(3):421-31. doi: 10.1111/j.1365-313X.2011.04882.x. Epub 2012 Jan 16.

15.

Conservation and divergence of microRNAs in Populus.

Barakat A, Wall PK, Diloreto S, Depamphilis CW, Carlson JE.

BMC Genomics. 2007 Dec 31;8:481. doi: 10.1186/1471-2164-8-481.

16.

Identification of plant microRNA homologs.

Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH.

Bioinformatics. 2006 Feb 1;22(3):359-60. Epub 2005 Nov 29.

PMID:
16317073
17.

TAM: a method for enrichment and depletion analysis of a microRNA category in a list of microRNAs.

Lu M, Shi B, Wang J, Cao Q, Cui Q.

BMC Bioinformatics. 2010 Aug 9;11:419. doi: 10.1186/1471-2105-11-419.

18.

Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data.

Yang X, Zhang H, Li L.

Genomics. 2011 Jul;98(1):40-6. doi: 10.1016/j.ygeno.2011.03.011. Epub 2011 Apr 4.

19.

Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.

German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ.

Nat Biotechnol. 2008 Aug;26(8):941-6. doi: 10.1038/nbt1417. Epub 2008 Jun 9.

PMID:
18542052
20.

MicroRazerS: rapid alignment of small RNA reads.

Emde AK, Grunert M, Weese D, Reinert K, Sperling SR.

Bioinformatics. 2010 Jan 1;26(1):123-4. doi: 10.1093/bioinformatics/btp601. Epub 2009 Oct 29.

PMID:
19880369

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