Hongyu Li

This paper develops LIME, a bacterial platform that engagers T and NK cells to target tumors, showing enhanced cytotoxicity and immune response in preclinical models.

This study evaluates foundation models for single-cell data analysis across eight tasks, finding that task-specific methods may outperform them in some cases and proposing guidelines for improving FM performance.

PERADIGM identifies rare disease-associated genes by integrating phenotype embeddings and patient similarity, outperforming traditional methods in detecting candidate genes for ADPKD, Marfan syndrome, and NF1.

The paper uses a Markov Random Field model with protein-protein interaction data to identify 46 candidate genes for congenital heart disease, including known and highly expressed genes.

The paper introduces MRFscRNAseq, a Markov Random Field model for identifying cell-type specific differentially expressed genes in scRNA-seq data, showing improved power over conventional methods.