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MiRank specifications


Unique identifier OMICS_07334
Name MiRank
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Weixiong Zhang

Publication for MiRank

MiRank citations


Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods

Sci Rep
PMCID: 5953923
PMID: 29765080
DOI: 10.1038/s41598-018-25578-3

[…] other approaches were also tested, e.g. Random Forest classifier was used in MiPred and was also chosen as best performing method in HuntMi. A novel Markov random walk based method was implemented in miRank, while deKmer is a quantum mechanics inspired method. Usually, new tools are developed with the use of enlarged feature sets and new, larger or improved data sets. Several studies emphasized on […]


Computational prediction of human disease related microRNAs by path based random walk

PMCID: 5601672
PMID: 28938576
DOI: 10.18632/oncotarget.17226

[…] ar phenotypes likely share common miRNA [–]. Therefore, different methods have been proposed to predict miRNA and disease association such as random walk-based methods. In 2008, Xu et al. [] proposed miRank, a ranking algorithm based on random walk. They tested their method on Homo sapiens genomes and achieved a good accuracy. In 2012, Chen et al. [] adopted a global network similarity measure and […]


Computational Approaches in Detecting Non Coding RNA

Curr Genomics
PMCID: 3861888
PMID: 24396270
DOI: 10.2174/13892029113149990005

[…] can predict known and novel miRNAs. Furthermore, it could provide detailed information for the known miRNAs, such as miRNA/miRNA* and absolute/relative reads count []. Here is another program called miRank using random walk-based ranking algorithm. The miRank method has some remarking properties. For example, it does not rely on cross-species conservation so that it can identify species-specific […]


Identifying miRNAs, targets and functions

Brief Bioinform
PMCID: 3896928
PMID: 23175680
DOI: 10.1093/bib/bbs075

[…] s because structures of known miRNA are used to train the learning processes to discriminate between true predictions and false positives [, ]. Many algorithms, for example, miRScan [], miRSeeker [], miRank [], miRDeep [], miRDeep2 [] and miRanalyzer [], have been proposed. Once predicted, experimental techniques such molecular cloning, sequencing or hybridization are typically used to validate th […]


MicroRNA Prediction Using a Fixed Order Markov Model Based on the Secondary Structure Pattern

PLoS One
PMCID: 3484136
PMID: 23118959
DOI: 10.1371/journal.pone.0048236

[…] e highly conserved motifs in 3′-UTRs . (4) Machine learning approaches include support vector machine (SVM), hidden Markov model (HMM) and naïve Bayes classifier (NBC), such as Triplet-SVM , MiPred , miRank , CID-miRNA , HHMMiR , CSHMM and MatureBayes . However, the first three approaches are poor to identify new miRNAs across species lack of homologies. Although the machine leaning approaches ac […]


siRNAs from miRNA sites mediate DNA methylation of target genes

Nucleic Acids Res
PMCID: 2978365
PMID: 20621980
DOI: 10.1093/nar/gkq590

[…] gram (). The rest steps of our method followed the same procedure in (), except the features used to build the support vector machines (SVM) classification model. All the features that we used in our miRank method () were adopted in the current study. In addition, we introduced several extra features based on the patterns of sRNA reads mapped to the known miRNA precursors. The first feature was th […]


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MiRank institution(s)
Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, MO, USA
MiRank funding source(s)
Supported in part by NSF grant IIS-0535257, a grant from the Alzheimer’s Association and a grant from Monsanto Corporation.

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