期刊
BRIEFINGS IN BIOINFORMATICS
卷 20, 期 5, 页码 1836-1852出版社
OXFORD UNIV PRESS
DOI: 10.1093/bib/bby054
关键词
miRNA; bioinformatics tools; text mining; bibliometric; ranking
资金
- Academy of Finland [62340]
- University of Macau Faculty of Health Sciences [MYRG2016-00101-FHS]
- National Natural Science Foundation of China [61472158, 61572228, 61602207]
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 similar to 1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or Page Rank 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.
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