Hua Yu

eRNAformer maps enhancer-derived RNA loci genome-wide using deep learning, identifying new eRNA loci linked to disease risk and cancer therapy.

KDDANet identifies hidden genes mediating known drug-disease associations by analyzing genome-wide functional gene interaction networks, revealing both known and novel candidates in diseases like Alzheimer's and obesity.

This paper introduces scMAGeCK, a computational framework for analyzing single-cell CRISPR screens to identify genes and non-coding elements associated with multiple phenotypes.

The paper constructs and analyzes RNA-seq-based gene co-expression networks in four plant species, identifying conserved and species-specific modules linked to biological functions and agronomic traits.

The paper builds a high-quality rice RNA-seq-based gene co-expression network using an ensemble method and demonstrates its utility for predicting gene function and regulation.