Hiroki Ueda

RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references, achieving high accuracy in genomic placement and transcript-level abundance estimation.

This paper introduces SCALE-CLIP, a method to generate comparable RBP binding maps, and defines a positional and combinatorial regulatory code for alternative splicing.

nanoDoc detects RNA modifications from Nanopore raw reads using deep one-class classification, achieving 0.96 AUC accuracy in E. coli and S. cerevisiae.