Lixin Ren

Resolving how genetic perturbations act through gene regulatory paths

REGA-perturb resolves gene regulatory paths from genetic perturbations using reference epigenomes and RNA measurements, outperforming existing methods in identifying TF-target relationships and predicting regulatory changes.

Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks

This paper introduces REGA, a framework that uses reference regulatory elements to infer gene regulatory networks from expression data, showing improved performance across multiple benchmarks and applications.

GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization

GuidingNet predicts DNA methyltransferase genome-wide binding by integrating multi-omics data and reveals transcriptional cofactors involved in methylation.