Trends in the development of miRNA bioinformatics tools

By Liang Chen, Liisa Heikkinen, Changliang Wang, Yang Yang, Huiyan Sun, Garry Wong. Briefings Bioinform., 2019

513 citations recorded by the source corpus.

Abstract 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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/13226c692dd6908c64555fb095c4ee968a539a83

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. Xiaowei Wang
2. Weijun Liu
3. Yuhao Chen
4. Jiuyong Li
5. Murray J. Cairns
6. Bing Liu

In Molecular Biology

1. Xiaowei Wang
2. Maoguang Zhang
3. Fei Liu
4. Jingyuan Yang
5. Xiangkang Jiang
6. Weijun Liu
7. Jiawei Tao
8. Yuhao Chen

Citations in the corpus

• The bioinformatics toolbox for circRNA discovery and analysis (2020, methodology): “Our previous study found that the circRNA tools and miRNA tools have a strong connection [127].”
• A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia (2022, methodology): “PageRank has been applied in medical domains with success [35, 36].”
• Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data (2019, background): “In particular, in recent years, new models have been developed based on breakthroughs in experimental methods as well as novel insights into the mechanisms of miRNA target regulation [6].”