DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. - Jiaxing Chen; Chinwang Cheong; Liang Lan; Xin Zhou; Jiming Liu 001; Aiping Lyu; William K. Cheung 001; Lu Zhang 061 (Briefings Bioinform., 2021)

A machine learning model for disease risk prediction by integrating genetic and non-genetic factors. - Yu Xu; Chonghao Wang; Zeming Li; Yunpeng Cai; Ouzhou Young; Aiping Lyu; Lu Zhang 061 (BIBM, 2022)

dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data. - Yu Xu; Jiaxing Chen; Aiping Lyu; William K. Cheung 001; Lu Zhang 061 (Briefings Bioinform., 2022)

Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute. - Ke Xu; Chinwang Cheong; Werner Pieter Veldsman; Aiping Lyu; William K. Cheung 001; Lu Zhang 061 (Briefings Bioinform., 2023)

Benchmarking multi-platform sequencing technologies for human genome assembly. - Jingjing Wang; Werner Pieter Veldsman; Xiaodong Fang; Yufen Huang; Xuefeng Xie; Aiping Lyu; Lu Zhang 061 (Briefings Bioinform., 2023)

An Interpretable AI framework Quantifying Traditional Chinese Medicine Principles Towards Enhancing and Integrating with Modern Biomedicine. - Haoran Li; Xingye Cheng; Ziyang Huang; Jingyuan Luo; Qianqian Xu; Qiguang Zhao; Tianchen Guo; Yumeng Zhang; Linda Lidan Zhong; Zhaoxiang Bian; Leihan Tang; Aiping Lyu; et al. (CoRR, 2025)