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Items: 1 to 20 of 98

1.

Semirna: searching for plant miRNAs using target sequences.

Muñoz-Mérida A, Perkins JR, Viguera E, Thode G, Bejarano ER, Pérez-Pulido AJ.

OMICS. 2012 Apr;16(4):168-77. doi: 10.1089/omi.2011.0115. Epub 2012 Mar 20.

PMID:
22433074
2.

MiRAuto: an automated user-friendly microRNA prediction tool utilizing plant small RNA sequencing data.

Lee J, Kim DI, Park JH, Choi IY, Shin C.

Mol Cells. 2013 Apr;35(4):342-7. doi: 10.1007/s10059-013-0019-8. Epub 2013 Apr 15.

3.

Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing.

Kim B, Yu HJ, Park SG, Shin JY, Oh M, Kim N, Mun JH.

BMC Plant Biol. 2012 Nov 19;12:218. doi: 10.1186/1471-2229-12-218.

4.

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.

5.

miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data.

An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC.

BMC Bioinformatics. 2014 Aug 12;15:275. doi: 10.1186/1471-2105-15-275.

6.

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets.

Wang XJ, Reyes JL, Chua NH, Gaasterland T.

Genome Biol. 2004;5(9):R65. Epub 2004 Aug 31.

7.

miRU: an automated plant miRNA target prediction server.

Zhang Y.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W701-4.

8.

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
9.

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.

10.
11.

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
12.

MTide: an integrated tool for the identification of miRNA-target interaction in plants.

Zhang Z, Jiang L, Wang J, Gu P, Chen M.

Bioinformatics. 2015 Jan 15;31(2):290-1. doi: 10.1093/bioinformatics/btu633. Epub 2014 Sep 24.

PMID:
25256573
13.

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.

14.

Bioinformatics Resource Manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools.

Tilton SC, Tal TL, Scroggins SM, Franzosa JA, Peterson ES, Tanguay RL, Waters KM.

BMC Bioinformatics. 2012 Nov 23;13:311. doi: 10.1186/1471-2105-13-311.

15.

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
16.

BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.

Chae H, Rhee S, Nephew KP, Kim S.

Bioinformatics. 2015 Jan 15;31(2):265-7. doi: 10.1093/bioinformatics/btu614. Epub 2014 Sep 29.

PMID:
25270639
17.

Computational prediction of the localization of microRNAs within their pre-miRNA.

Leclercq M, Diallo AB, Blanchette M.

Nucleic Acids Res. 2013 Aug;41(15):7200-11. doi: 10.1093/nar/gkt466. Epub 2013 Jun 8.

18.

Computational prediction and experimental verification of miRNAs in Panicum miliaceum L.

Wu Y, Du J, Wang X, Fang X, Shan W, Liang Z.

Sci China Life Sci. 2012 Sep;55(9):807-17. Epub 2012 Sep 27.

PMID:
23015130
19.

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
20.

Computational identification of microRNAs and their targets in perennial Ryegrass (Lolium perenne).

Huang Y, Zou Q, Sun XH, Zhao LP.

Appl Biochem Biotechnol. 2014 Jun;173(4):1011-22. doi: 10.1007/s12010-014-0891-5. Epub 2014 Apr 22.

PMID:
24752936

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