Yujia Cai

Agentic Discovery Transfer Enables Cross-Cancer Discovery at Scale

SMART, a multi-agent framework, transfers findings from single-cell RNA-sequencing cancer studies to other cancer types, identifying cross-cancer prognostic signatures and generating new hypotheses.

CD3, CD28, TCRαβ expression and IL-2 production in a spontaneous glycosylphosphatidylinositol-deficient Jurkat T cell line

This study examines the effects of GPI-deficiency on TCR, CD3, CD28 expression and IL-2 production in a GPI-deficient Jurkat T cell line, finding altered surface receptor expression but no significant impairment in IL-2 production under direct pathway activation.

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

AutoZyme optimizes bioinformatics software by autonomously identifying and applying code changes to improve runtime without significant memory use.

CASSIA: a multi-agent large language model for reference free, interpretable, and automated cell annotation of single-cell RNA-sequencing data

CASSIA automates and improves cell type annotation in single-cell RNA-sequencing data with interpretability and accuracy.

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

This paper introduces a data-driven method to detect functional proteoform groups from bottom-up proteomic datasets, identifying state-specific proteoform groups linked to molecular mechanisms.