Wei‐Shinn Ku

RiboRep predicts codon-resolved ribosome density by integrating RNA sequences and ribosome occupancy signals using a cross-modal transformer framework, achieving strong performance across multiple species.

PAG-Agent performs pathway-level analysis and interpretation of transcriptomic data, identifying biologically relevant pathways and generating hypotheses across datasets and conditions.

The paper introduces todenE, a clustering method combining topology and density-based approaches to group PAGs into Super-PAGs, improving functional representation in genomics.