The amount of biological sequence data has increased dramatically due to the advancement of high-throughput sequencing technologies. There are many hurdles in managing and analyzing this data to determine its biological and medical implications. AI technology provides a powerful answer to bioinformatics research as well as new data analysis tools for computational biology and bioinformatics data analysis. The main uses of AI in bioinformatics research are: creating more effective AI tools to solve biological problems and exploiting the biological significance found in large biological data using existing AI technology.

To get a more precise interpretation, AI assistance is still required for many biological issues. These pressing issues encompass, among other things: 1) comprehensive transcriptomics, genomics, proteomics, and epigenomics data analysis; 2) functional prediction of first-order sequence data; 3) multiple omics fusion data analysis; 4) emerging single-cell data analysis; and 5) common issues that AI encounters in biological big data analysis, such as data imbalance and interpretable deep learning models, among others. The most recent developments in AI applications in bioinformatics, both in terms of methodologies and strategies as well as AI solutions for biological data security, will be the main topics of this Special Issue.