Overall workflow of DARTS. Nature Methods, 2019.

The Xing lab develops novel computational tools for studying RNA processing and modifications using high-throughput data. Our lab developed rMATS (replicate Multivariate Analysis of Transcript Splicing), a tool for discovering and quantifying alternative splicing events using short-read RNA-seq data. rMATS is widely used, as evidenced by >3,000 citations to date and by its adoption as the splicing analysis tool in the recent ENCODE3 RNA milestone study.

We also developed DARTS (Deep-learning Augmented RNA-seq analysis of Transcript Splicing), a deep-learning model leveraging consortium-scale RNA-seq data (ENCODE, Roadmap Epigenomics) to improve the precision of RNA-seq-based alternative splicing analysis. Ongoing work in our lab includes building new tools upon and improving both the rMATS and DARTS pipelines.