# | Name | Description | Organism Specific |
Data Collection | Data AvailableFor Download | References |
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1 | ADmiRE | Annotative Database of miRNA Elements is a miRNA variant annotation tool which combines miRNA sequence features derived from conservation and variation with biologically important annotations. Framework for microRNA variant annotation and prioritization using human population and disease datasets. | Homepage Publication Oct. 10, 2018 Citations: 12 | |||
2 | Antagomirbase | A database based on putative antagomirs-miRNA heterodimers. In this work, the human miRNA dataset was used as template to design putative antagomirs, using GC content and secondary structures as parameters. The algorithm used predicted the free energy of unbound antagomirs. | Homepage Publication Aug. 20, 2011 Citations: 1 | |||
3 | CircuitsDB2 | CircuitsDB 2 contains a large number of regulatory circuits, composed by Transcription Factors, target genes, microRNAs and lincRNAs interacting together, in the human genome. The resulting integrated network can be the starting point for a deeper understanding of their system-level properties and provides candidates for experimental validation. | Homepage Publication Aug. 23, 2010 Citations: 71 | |||
4 | CoGemiR | CoGeMiR is a publicily available microRNA-centered database whose aim is to offer an overview of the conservation of microRNAs during evolution in different animal species. This database collects information on genomic location, conservation and expression data of both known and predicted microRNAs. | Homepage Publication Oct. 6, 2008 Citations: 13 | |||
5 | CREAM | CREAM (Chemotherapy ResistancE-Associated MiRSNP Database) is a free online database depositing the functional miRSNP associated with chemotherapy resistance. | Homepage Publication May 29, 2014 Citations: 2 | |||
6 | dbDEMC 2.0 | dbDEMC (database of Differentially Expressed MiRNAs in human Cancers) is an integrated database that designed to store and display differentially expressed microRNAs (miRNAs) in human cancers detected by high-throughput methods. In this updated version of dbDEMC, a total of 209 expression profiling data sets across 36 cancer types and 73 subtypes, and a total of 2224 differentially expressed miRNAs were identified. | Homepage Publication Jan. 4, 2017 Citations: 136 | |||
7 | DIANA-LncBase v2 | DIANA-LncBase is first extensive database dedicated to cataloging miRNA:lncRNA interactions, providing the largest collection of experimentally supported and in silico predicted MREs on lncRNAs. | Homepage Publication Nov. 26, 2015 Citations: 358 | |||
8 | DIANA-TarBase | Provides for the first time hundreds of thousands of high quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. With DIANA-TarBase v7.0 you can easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments | Homepage Publication Nov. 21, 2014 Citations: 369 | |||
9 | DMD | The Dietary microRNA Database is a searchable database of published and novel microRNA sequences discovered in human food. The annotation covers the hairpin structure of the pre-microRNAs, cross-species sequence comparison on each mature microRNA, reported disease relevance, and the experimentally validated gene targets, of which a gene regulation network was built for each entry. DMD can be also used to generate a list of features for use in machine learning applications. It is split up into two major categories: Primary, and Secondary. The Primary features are all sequence based features while the Secondary features are based on structural attributes. | Homepage Publication June 1, 2015 Citations: 13 | |||
10 | EpimiR | EpimiR comprehensive database which store the experimentally validated mutual regulations between epigenetic modifications and miRNAs. | Homepage Publication March 28, 2014 Citations: 24 | |||
11 | EpimiRBase | EpimiRBase is a manually curated databasefor researchers interested in the role of microRNAs in epilepsy. The fully-searchable database includes information on up- and downregulated microRNAs in the brain and blood, as well as functional studies, and covers both rodent models and human epilepsy. | Homepage Publication Jan. 8, 2016 Citations: 22 | |||
12 | ExcellmiRDB | A curated online database that provides integrated information about miRNAs levels in biofluids in a user-friendly way. Although many miRNA databases, including disease-oriented databases, have been launched before, the ExcellmiRDB is so far the only one specialized for storing curated data on miRNA levels in biofluid samples. | Homepage Publication Jan. 6, 2015 Citations: 8 | |||
13 | HMDD | A repository of miRNA-associated diseases, obtained by manual curation from literature data. HMDD v2.0 presents more detailed and comprehensive annotations to the human miRNA-disease association data, including miRNA-disease association data from the evidence of genetics, epigenetics, circulating miRNAs, and miRNA-target interactions. | Homepage Publication Nov. 4, 2013 Citations: 335 | |||
14 | HOCTARdb | The HOCTAR database (db) is a publicly available resource collecting ranked list of predicted target genes for 290 intragenic miRNAs annotated in human. HOCTARdb is a unique resource that integrates miRNA target prediction genes and transcriptomic data to score putative miRNA targets looking at the expression behavior of their host genes. | Homepage Publication March 22, 2011 Citations: 29 | |||
15 | mESAdb | A regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. | Homepage Publication Dec. 22, 2010 Citations: 14 | |||
16 | MicroCosm Targets | A web resource developed by the Enright Lab at the EMBL-EBI containing computationally predicted targets for microRNAs across many species. | Homepage Publication Dec. 23, 2007 Citations: 2114 | |||
17 | microPIR2 | MicroPIR2 is public database containing over 80 and 40 million predicted microRNA target sites located within human and mouse promoter sequences. These predicted targets are presented along with their related genomic and experimental data. | Homepage Publication Nov. 25, 2014 Citations: 7 | |||
18 | microRNA.org | A comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. | Homepage Publication Dec. 23, 2007 Citations: 1337 | |||
19 | microRNAviewer / miRviewer | miRviewer provides a comprehensive view of all known miRNAs in annotated animal genomes. microRNAviewer exhibits a comprehensive set of miRNA genes both from miRBase and candidate homologs identified using miRNAminer. Additional layers of information, such as conservation, multiple alignments of the sequences, indication of mutated miRNAs, genomic loci and secondary structure, are also available. | Homepage Publication Feb. 13, 2012 Citations: 37 | |||
20 | mimiRNA | A database of miRNA expression profile data across different tissues and cell lines. mimiRNA incorporates a sample classification algorithm, ExParser, that groups identical miRNA or mRNA experiments from separate sources. This enables mimiRNA to provide reliable expression profiles and to discover functional relations between miRNAs and mRNAs such as miRNA targets. | Homepage Publication Nov. 17, 2009 Citations: 39 | |||
21 | miR2Disease | miR2Disease, a manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Each entry contains detailed information on a miRNA-disease relationship, including miRNA ID, disease name, a brief description of the miRNA-disease relationship, miRNA expression pattern in the disease state, detection method for miRNA expression, experimentally verified miRNA target gene(s), and literature reference. | Homepage Publication Jan. 1, 2009 Citations: 625 | |||
22 | miRandola | A comprehensive classification of different extracellular circulating miRNA types. A direct link to the knowledge base miRò together with the inclusion of datamining facilities allow users to infer possible biological functions of the circulating miRNAs and their connection with the phenotype. | Homepage Publication Oct. 19, 2012 Citations: 79 | |||
23 | miRBase | The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. | Homepage Publication Nov. 25, 2013 Citations: 2519 | |||
24 | miRBase Tracker | miRBase Tracker is a framework on top of miRBase that, in addition to providing miRBase's basic annotation information, allows researchers to keep track of miRNA annotation changes and facilitates reannotation. | Homepage Publication Aug. 24, 2014 Citations: 46 | |||
25 | miRCancer | miRCancer provides comprehensive collection of microRNA (miRNA) expression profiles in various human cancers which are automatically extracted from published literatures in PubMed. It utilizes text mining techniques for information collection. Manual revision is applied after auto-extraction to provide 100% precision. | Homepage Publication Jan. 16, 2013 Citations: 209 | |||
26 | miRDB | Recently updated features of miRDB, includes 2.1 million predicted gene targets regulated by 6709 miRNAs. In addition to presenting precompiled prediction data, a new feature is the web server interface that allows submission of user-provided sequences for miRNA target prediction. In this way, users have the flexibility to study any custom miRNAs or target genes of interest. | Homepage Publication Nov. 5, 2014 Citations: 943 | |||
27 | miRdSNP | A database of manually curated dSNPs on the 3'UTRs of human genes from available publications in PubMed. The advanced web interface allows users to perform proximity searches between miRNA target sites and dSNPs by gene name, miRbase ID, target prediction algorithm, disease, and any nucleotide distance between dSNPs and miRNA target sites. | Homepage Publication Jan. 25, 2012 Citations: 76 | |||
28 | miRecords | A resource for animal miRNA-target interactions. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. | Homepage Publication Jan. 1, 2009 Citations: 705 | |||
29 | miREnvironment | miREnvironment is a database that curated and collected experimentally supported microRNA (miRNA), one class of newly identified genetic factors, and environmental factor interplays and their associated phenotypes. It also has a tool performing bioinformatic analysis to predict the result of cancer treatment and associations between EFs and human disease. | Homepage Publication Oct. 7, 2011 Citations: 31 | |||
30 | mirEX 2.0 | mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. | Homepage Publication June 16, 2015 Citations: 33 | |||
31 | miRGate | miRGate is a curated database of human, mouse and rat miRNAs/mRNAs targets. It is designed to analyze miRNA and gene isoforms lists under a common and consistent space of annotations. Including all existing 3 UTR and the entirely known miRNAs. All Havana biotypes and ENCODE principal isoforms for the three organisms are also included. | Homepage Publication April 8, 2015 Citations: 44 | |||
32 | miRGator | Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools. By keeping datasets and analytic tools up-to-date, miRGator should continue to serve as an integrated resource for biogenesis and functional investigation of miRNAs. | Homepage Publication Nov. 27, 2012 Citations: 76 | |||
33 | DIANA-miRGen v3.0 | Aim of DIANA-miRGen v3.0 is to provide for the first time accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation. The database currently supports 276 miRNA TSSs that correspond to 428 precursors and >19M binding sites of 202 TFs on a genome-wide scale in nine cell-lines and six tissues of Homo sapiens and Mus musculus. | Homepage Publication Nov. 19, 2015 Citations: 27 | |||
34 | MirGeneDB.org | MirGeneDB.org is the curated microRNA gene database that We established MirGeneDB —to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire. Currently entries for human, mouse, zebra fish and chicken are available. Expansion is planned for summer 2017 | Homepage Publication Sept. 1, 2015 Citations: 264 | |||
35 | miRNA SniPer | An online tool for the detection of miRNA polymorphisms in vertebrates. miRNA SNiPer accepts a list of miRNA genes and returns a table of variations within different regions of miRNA genes: pre-miRNA, mature, seed region. | Homepage Publication Jan. 27, 2012 Citations: 31 | |||
36 | miRNA - Target Gene Prediction at EMBL | This database provides access to the 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs. | Homepage Publication Feb. 15, 2005 Citations: 957 | |||
37 | miRNAMap | miRNAMap 2.0 collects experimentally verified microRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes. Three computational tools, miRanda, RNAhybrid and TargetScan, were employed to identify miRNA targets in 3'-UTR of genes as well as the known miRNA targets. Additionally, miRNA expression profiles can provide valuable clues on the characteristics of miRNAs, including tissue specificity and differential expression in cancer/normal cell. | Homepage Publication Dec. 23, 2007 Citations: 140 | |||
38 | miRNEST | A integrative collection of animal, plant and virus microRNA data. In its updated version miRNEST 2.0, the database is complemented with our extensive miRNA predictions from deep sequencing libraries, data from plant degradome analyses, results of pre-miRNA classification with HuntMi and miRNA splice sites information. | Homepage Publication Nov. 15, 2013 Citations: 26 | |||
39 | miROrtho | miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. | Homepage Publication Jan. 1, 2009 Citations: 41 | |||
40 | miRPathDB | miRPathDB aim to augment available target pathway web-servers by providing researches easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific the regulations are. The database contains a large number of miRNAs, different miRNA target sets and a broad selection of functional biochemical categories. In addition to H. sapiens, also M. musculus data are stored and can be compared to human target pathways. | Homepage Publication Oct. 13, 2016 Citations: 61 | |||
41 | mirPub | mirPub is a database and a related web application which provides a powerful and intuitive interface to the researchers that want to search for publications related to particular microRNA molecules. mirPub also provides useful information about the correlation of these microRNAs to any diseases, tissues and genes. It facilitates publication search by considering microRNA families and the history of the microRNA nomenclature. | Homepage Publication Dec. 20, 2014 Citations: 12 | |||
42 | miRSel | Automated extraction of associations between microRNAs and genes from the biomedical literature. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO) terms. | Homepage Publication March 16, 2010 Citations: 36 | |||
43 | MirSNP | MirSNP is a collection of human SNPs in predicted miRNA-mRNA binding sites. | Homepage Publication Nov. 23, 2012 Citations: 121 | |||
44 | miRStress | The miRStress database is a comprehensive resource that documents microRNA deregulation following exposure to different stress stimuli. | Homepage Publication Nov. 14, 2013 Citations: 13 | |||
45 | miRSystem | A database which integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan. This database contains validated data from TarBase and miRecords on interaction between miRNA and its target genes. | Homepage Publication Aug. 1, 2012 Citations: 156 | |||
46 | miRTarBase | miRTarBase provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. | Homepage Publication Nov. 20, 2015 Citations: 544 | |||
47 | miRWalk | A publicly available comprehensive resource, hosting the predicted as well as the experimentally validated microRNA (miRNA)-target interaction pairs. | Homepage Publication July 30, 2015 Citations: 678 | |||
48 | MtiBase | MtiBase (MiRNA-target interactions database) is a database that identify CDS-located and 5'UTR-located miRNA binding sites and systematically evaluate miRNA regulatory effects on mRNA stability and translation by integrating multiple high-throughput experimental datasets such as Ago CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH), mRNA profiles, ribisome-protected fragment sequencing (RPF) and pulsed stable isotope labeling with amino acids in culture (pSILAC). The SNP influence to the regulatory effects of CDS-located and 5'UTR-located miRNA binding sites was also systematically investigated. | Homepage Publication Oct. 1, 2015 Citations: 18 | |||
49 | multiMiR | A miRNA-target interaction R package and database, which includes: (i) compilation of nearly 50 million records in human and mouse from 14 different databases, more than any other collection; (ii) expansion of databases to those based on disease annotation and drug microRNA response, in addition to many experimental and computational databases; and (iii) user-defined cutoffs for predicted binding strength to provide the most confident selection. | Homepage Publication July 24, 2014 Citations: 252 | |||
50 | OncomiRDB | oncomiRDB database aimes at annotating the experimentally verified oncogenic and tumor-suppressive miRNAs from literature. This database only collects items having direct functional evidences: 1) the miRNA regulates at least one cancer-related phenotype or cellular process (such as proliferation, apoptosis, migration and invasion, senescence and cell cycle regulation); or 2) the miRNA directly regulates at least one oncogenic or tumor-suppressive gene verified by luciferase reporter assay. | Homepage Publication March 20, 2014 Citations: 59 | |||
51 | OncomiRdbB | OncomiRdbB is an integrated database consisting of the miRNAs of human and mouse genomes, their sequences, chromosome and gene locations, respective targets and their description, pathways it regulates in breast cancer.The miRNAs were mined from miRBase, Phenomir, Mir2Disease etc and their respective sequences were obtained from miRbase. Their target genes were computationally derived from different oncogenic pathways such as wnt, Jak- Stat, MAPK, mTOR, VEGF, Apoptosis and Notch pathways and their genomic sequences from ENSEMBLE- BioMart. Additionally, we have also listed the experimentally validated novel microRNAs for human breast cancer. | Homepage Publication Jan. 15, 2014 Citations: 6 | |||
52 | PASmiR | PASmiR, a literature-curated and web-accessible database, was developed to provide a solid platform for collection, standardization, and searching of these miRNA-stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses in the plant stress physiology community. | Homepage Publication March 1, 2013 Citations: 28 | |||
53 | PhenomiR | The PhenomiR database provides information about differentially regulated miRNA expression in diseases and other biological processes. The content of PhenomiR is completely generated by manual curation of experienced annotators. The design principle of PhenomiR is to use established ontologies and resources. | Homepage Publication Jan. 20, 2010 Citations: 122 | |||
54 | PmiRExAt | PmiRExAt is a new online web resource that provides the most comprehensive comparative view yet of plant microRNAs (miRNAs) expression in multiple tissues, developmental stages of wheat, rice and maize. Meta-analysis of the publicly available small RNA datasets showed significant expression patterns of several miRNAs. This web resource and service can be used by plant science community to study expression patterns of miRNAs. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. | Homepage Publication April 13, 2016 Citations: 14 | |||
55 | PMTED | PMTED is designed to retrieve and analyze expression profiles of miRNA targets represented in the plethora of existing microarray data that are manually curated. It provides a Basic Information query function for plant miRNAs and their target sequences, gene ontology, and differential expression profiles. | Homepage Publication June 3, 2013 Citations: 13 | |||
56 | PNRD | It is the updated version of PMRD. PNRD mainly focuses on plant species. A total of 25739 entries of 11 different types of ncRNAs from 150 plant species were collected. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. | Homepage Publication Nov. 14, 2014 Citations: 84 | |||
57 | PolymiRTS Database | An integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. The browse and search pages of PolymiRTS allow users to explore the relations between the PolymiRTSs and gene expression traits, physiological and behavioral phenotypes, human diseases and biological pathways. | Homepage Publication Oct. 24, 2013 Citations: 148 | |||
58 | PuTmiR | Focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. | Homepage Publication April 15, 2010 Citations: 25 | |||
59 | SomamiR DB 2.0 | SomamiR is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). It also provides an integrated platform for the functional analysis of these somatic mutations. Additionally, the SomamiR DB contains a collection of somatic and germline mutations in miRNAs or their target sites that have been strongly linked with cancer. Specifically, the majority of these mutations met the following criteria (a) they have been associated with cancer risk in GWAS or CGAS and (b) there is experimental evidence indicating that the mutation alters miRNA function | Homepage Publication Nov. 17, 2015 Citations: 63 | |||
60 | starBase | It is designed for decoding Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq data and tumor samples. starBase is also developed for deciphering Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from CLIP-Seq datasets. | Homepage Publication Dec. 1, 2013 Citations: 2419 | |||
61 | targetHub | A CouchDB database of miRNA-gene interactions. TargetHub provides a programmer-friendly interface to access miRNA targets. The Web site provides RESTful access to miRNA-gene interactions with an assortment of gene and miRNA identifiers. It can be a useful tool to integrate miRNA target interaction data directly into high-throughput bioinformatics analyses. | Homepage Publication Sept. 6, 2013 Citations: 10 | |||
62 | TargetScanS | Database of microRNA targets conserved in 5 vertebrates. | Homepage Publication Jan. 14, 2005 Citations: 5529 | |||
63 | TMREC | TMREC provides the detailed cascade regulations of TF-miRNA in the context of human diseases, which enable the experimental biologist to understand the transcriptional and post-transcriptional regulatory mechanisms in specific disease, and identify the potential therapeutic targets in the upstream of the cascades. | Homepage Publication May 1, 2015 Citations: 10 | |||
64 | TransmiR | A database for transcription factor-microRNA regulations. | Homepage Publication Sept. 28, 2009 Citations: 206 | |||
65 | Vir-Mir db | Vir-Mir database, a database containing predicted viral miRNA candidate hairpins. | Homepage Publication Dec. 23, 2007 Citations: 31 | |||
66 | VIRmiRNA | VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. | Homepage Publication Nov. 7, 2014 Citations: 49 | |||
67 | ViTa | ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC, etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also provide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons. | Homepage Publication Jan. 3, 2007 Citations: 46 | |||
68 | YM500v2 | YM500 is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from small RNA sequencing (smRNA-seq). In this update of YM500, we focus on the cancer miRNAome to make the database more disease-orientated. | Homepage Publication Nov. 14, 2014 Citations: 32 |