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Trends in the development of miRNA bioinformatics tools
Liang Chen; Liisa Heikkinen; Changliang Wang; Yang Yang; Huiyan Sun; Garry Wong
Source PublicationBriefings in Bioinformatics

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and 1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.

KeywordMirna Bioinformatics Tools Text Mining Bibliometric Ranking
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Document TypeJournal article
CollectionFaculty of Health Sciences
Corresponding AuthorGarry Wong
AffiliationFaculty of Health Sciences, University of Macau, E12 Avenida da Universidade, Taipa, Macau S.A.R., China
Corresponding Author AffilicationFaculty of Health Sciences
Recommended Citation
GB/T 7714
Liang Chen,Liisa Heikkinen,Changliang Wang,et al. Trends in the development of miRNA bioinformatics tools[J]. Briefings in Bioinformatics,2018,2018:1-17.
APA Liang Chen,Liisa Heikkinen,Changliang Wang,Yang Yang,Huiyan Sun,&Garry Wong.(2018).Trends in the development of miRNA bioinformatics tools.Briefings in Bioinformatics,2018,1-17.
MLA Liang Chen,et al."Trends in the development of miRNA bioinformatics tools".Briefings in Bioinformatics 2018(2018):1-17.
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