Review papers

Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression.

Mullany LE, Wolff RK, Slattery ML. 2015. Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression.. Cancer Inform. 14:121-30.

Contribution of bioinformatics prediction in microRNA-based cancer therapeutics.

Banwait JK, Bastola DR. 2015. Contribution of bioinformatics prediction in microRNA-based cancer therapeutics.. Adv Drug Deliv Rev. 81:94-103.

Common features of microRNA target prediction tools.

Peterson SM, Thompson JA, Ufkin ML, Sathyanarayana P, Liaw L, Congdon CBates. 2014. Common features of microRNA target prediction tools.. Front Genet. 5:23.

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction.

Srivastava PK, Moturu TRamji, Pandey P, Baldwin IT, Pandey SP. 2014. A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction.. BMC Genomics. 15:348.

Computational Methods for MicroRNA Target Prediction.

Ekimler S, Sahin K. 2014. Computational Methods for MicroRNA Target Prediction.. Genes (Basel). 5(3):671-83.

Computational methods for microRNA target prediction.

Hamzeiy H, Allmer J, Yousef M. 2014. Computational methods for microRNA target prediction.. Methods Mol Biol. 1107:207-21.

Web resources for microRNA research.

Schmitz U, Wolkenhauer O. 2013. Web resources for microRNA research.. Adv Exp Med Biol. 774:225-50.

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role.

Kleftogiannis D, Korfiati A, Theofilatos K, Likothanassis S, Tsakalidis A, Mavroudi S. 2013. Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role.. J Biomed Inform. 46(3):563-73.

Online resources for miRNA analysis.

Vlachos IS, Hatzigeorgiou AG. 2013. Online resources for miRNA analysis.. Clin Biochem. 46(10-11):879-900.

Advances in the techniques for the prediction of microRNA targets.

Zheng H, Fu R, Wang J-T, Liu Q, Chen H, Jiang S-W. 2013. Advances in the techniques for the prediction of microRNA targets.. Int J Mol Sci. 14(4):8179-87.

Enrichment analysis of miRNA targets.

Xu J, Wong C-W. 2013. Enrichment analysis of miRNA targets.. Methods Mol Biol. 936:91-103.

A Review of Computational Tools in microRNA Discovery.

Gomes CPC, Cho J-H, Hood L, Franco OL, Pereira RW, Wang K. 2013. A Review of Computational Tools in microRNA Discovery.. Front Genet. 4:81.

Benchmark comparison of ab initio microRNA identification methods and software.

Hu LL, Huang Y, Wang QC, Zou Q, Jiang Y. 2012. Benchmark comparison of ab initio microRNA identification methods and software.. Genet Mol Res. 11(4):4525-38.

One decade of development and evolution of microRNA target prediction algorithms.

Reyes-Herrera PH, Ficarra E. 2012. One decade of development and evolution of microRNA target prediction algorithms.. Genomics Proteomics Bioinformatics. 10(5):254-63.

Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data.

Yang X, Li L. 2012. Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data.. Biology (Basel). 1(2):297-310.

Evaluation of online miRNA resources for biomedical applications.

Gana NHTan, Victoriano AFB, Okamoto T. 2012. Evaluation of online miRNA resources for biomedical applications.. Genes Cells. 17(1):11-27.

Computational analysis of noncoding RNAs.

Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. 2012. Computational analysis of noncoding RNAs.. Wiley Interdiscip Rev RNA. 3(6):759-78.

Computational methods for ab initio detection of microRNAs.

Allmer J, Yousef M. 2012. Computational methods for ab initio detection of microRNAs.. Front Genet. 3:209.

Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression.

Dassi E, Quattrone A. 2012. Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression.. RNA Biol. 9(10):1224-32.

Finding microRNA targets in plants: current status and perspectives.

Ding J, Zhou S, Guan J. 2012. Finding microRNA targets in plants: current status and perspectives.. Genomics Proteomics Bioinformatics. 10(5):264-75.

Search miRNA Tools

Brief Introduction

Our database aim to make it easy for researchers to find the right tools or data source for their own specific study in miRNA field. Now we have collect >1000 tools. This database will update when every new 100 tools add in. Last update time 22nd April, 2018 (v1.2).

Updates History:

v1.1: 15th September, 2017 (970 tools)
v1.0: 1st October, 2016 (883 tools)

Latest Tools

	Tiresias
	Director
	EPLMI
	contextMMIA
	RISE

Popular Tools

	miRBase
	Rfam
	MiRscan
	miRanda (microRNA.org)
	TargetScan
	miRNA - Target Gene Prediction at EMBL
	PicTar
	RNAhybrid
	RNAz
	ViennaRNA
	DIANA-TarBase
	miRDeep
	smiRNAdb
	DIANA-microT
	PITA