Jianqi She

The paper benchmarks 16 teRNA analysis tools using simulated and real datasets, identifies performance trade-offs at different levels, and provides guidelines and a pipeline for best practices.

The paper develops TEITbase, a database of TE-initiated transcripts in 33 cancer types, identifying 38,995 transcripts and 6,203 tumor-specific ones, with tools for downstream analysis.

The paper identifies TE-initiated transcripts across human tissues and embryonic stem cells, showing tissue-specific activation and primate-specific TSSs contributing to gene regulation.

DEBKS detects differentially expressed circular RNAs by analyzing back-splicing events in RNA-seq data, showing efficiency and accuracy through real and simulated data.