Zongliang Yue

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.

MondrianMap provides multi-resolution visualization of gene set enrichment results, revealing directional oppositions and temporal dynamics across biological processes in cancer, aging, and exercise data.

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

This paper introduces ET-RAG, a RAG framework that improves biomedical question answering by incorporating evidence quality and recency into retrieval scoring, outperforming standard cosine similarity and full-context baselines.

GOALS introduces a novel framework for analyzing Gene Ontologies by discretizing them into optimal layers to enhance functional insights and visualization in biological processes.

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

This paper introduces GTKM, a method for visualizing gene expression data in glioblastoma, showing it identifies gene patterns linked to clinical outcomes and subtypes.