Ying Chen

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

Bambu-Clump improves transcript discovery and quantification from single-cell and spatial long-read RNA-seq data by leveraging cell and cluster information.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

This study constructs synthetic rDNA arrays in budding yeast and shows that reducing copy numbers or dispersing arrays does not harm cell growth or transcriptomes.

Bambu improves transcript quantification from long-read RNA-Seq by using context-aware annotations, enhancing precision without sacrificing sensitivity.

AERON quantifies transcript expression and detects gene-fusions from long RNA reads, showing accuracy on simulated and real data.