Classification of Schizophrenia by Iterative Random Forest Feature Selection Based on DNA Methylation Array Data. - Xinyu Hu; Min Li 007; Linconghua Wang; Xingyi Li 003; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

DualRank: multiplex network-based dual ranking for heterogeneous complex disease analysis. - Xingyi Li 003; Ju Xiang; Xinyu Hu; Fang-Xiang Wu; Min Li 007 (BIBM, 2019)

Identification of Prognostic and Heterogeneous Breast Cancer Biomarkers Based on Fusion Network and Multiple Scoring Strategies. - Xingyi Li 003; Ju Xiang; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (ICIC (2), 2019)

A topological AUC-based biomarker ensemble method for the complex disease analysis. - Xingyi Li 003; Ju Xiang; Fang-Xiang Wu; Min Li 007 (BIBM, 2020)

Network-based methods for predicting essential genes or proteins: a survey. - Xingyi Li 003; Wenkai Li; Min Zeng; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2020)

NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. - Ju Xiang; Jiashuai Zhang; Ruiqing Zheng; Xingyi Li 003; Min Li 007 (Briefings Bioinform., 2021)

FUNMarker: Fusion Network-Based Method to Identify Prognostic and Heterogeneous Breast Cancer Biomarkers. - Xingyi Li 003; Ju Xiang; Jianxin Wang 001; Jinyan Li 001; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A multi-source fusion method to identify biomarkers for breast cancer prognosis based on dual-layer heterogeneous network. - Xingyi Li 003; Zhelin Zhao; Ju Xiang; Jialu Hu; Xuequn Shang 001 (BIBM, 2022)

SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data. - Xingyi Li 003; Min Li 007; Ju Xiang; Zhelin Zhao; Xuequn Shang 001 (Bioinform., 2022)

A Dual Ranking Algorithm Based on the Multiplex Network for Heterogeneous Complex Disease Analysis. - Xingyi Li 003; Ju Xiang; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A personalized pathway activation inference method based on pathway structure for classification of inflammatory bowel disease. - Xingyi Li 003; Xuequn Shang 001; Zhelin Zhao; Chenzhuo Yan (BIBM, 2023)

Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks. - Xingyi Li 003; Jialuo Xu; Junming Li; Jia Gu; Xuequn Shang 001 (Briefings Bioinform., 2024)

Multiplex Networks and Pan-Cancer Multiomics-Based Driver Gene Identification Using Graph Neural Networks. - Xingyi Li 003; Junming Li; Jun Hao; Xingyu Liao; Min Li 007; Xuequn Shang 001 (Big Data Min. Anal., 2024)

Scbean: a python library for single-cell multi-omics data analysis. - Haohui Zhang; Yuwei Wang; Bin Lian; Yiran Wang; Xingyi Li 003; Tao Wang 082; Xuequn Shang 001; Hui Yang; Ahmad Aziz; Jialu Hu (Bioinform., 2024)

Deep graph convolutional network-based multi-omics integration for cancer driver gene identification. - Yingzhuo Wu; Jialuo Xu; Junming Li; Jia Gu; Xuequn Shang 001; Xingyi Li 003 (Briefings Bioinform., 2025)

PathActMarker: an R package for inferring pathway activity of complex diseases. - Xingyi Li 003; Jun Hao; Zhelin Zhao; Junming Li; Xingyu Liao; Min Li 007; Xuequn Shang 001 (Frontiers Comput. Sci., 2025)