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.

中文翻译：

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miRNA生物信息学工具发展趋势。

MicroRNA（miRNA）是小的非编码RNA，它们通过识别同源序列以及干扰转录，翻译或表观遗传过程来调节基因表达。为miRNA研究而开发的生物信息学工具包括用于miRNA预测和发现，结构，分析和靶标预测的工具。自2003年以来，我们手动整理了95篇评论论文和约1000种miRNA生物信息学工具。我们根据引文数量或PageRank得分对它们进行分类和排名，然后进行网络分析和文本挖掘（TM）研究miRNA工具的发展趋势。观察到了五个主要趋势：（1）在过去十年中，miRNA的识别和目标预测一直是热点；（2）手工管理和TM是从文献中收集miRNA知识的主要方法；（3）大多数早期工具维护良好并得到广泛使用；（4）经典机器学习方法保留了其实用性；然而，新颖的已经开始出现。（5）与疾病相关的miRNA工具正在出现。我们的分析为miRNA工具的过去发展和未来方向提供了重要的见识。