Identifying overlapping mutated driver pathways by constructing gene networks in cancer. - Hao Wu 062; Lin Gao 006; Feng Li 033; Fei Song; Xiaofei Yang 003; Nikola K. Kasabov (BMC Bioinform., 2015)

Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks. - Peizhuo Wang; Lin Gao 006; Yuxuan Hu 004; Feng Li 033 (BMC Bioinform., 2018)

Dual Sparse Collaborative Matrix Factorization Method Based on Gaussian Kernel Function for Predicting LncRNA-Disease Associations. - Ming-Ming Gao; Zhen Cui; Ying-Lian Gao; Feng Li 033; Jin-Xing Liu 001 (ICIC (3), 2019)

Inferring Communities and Key Genes of Triple Negative Breast Cancer Based on Robust Principal Component Analysis and Network Analysis. - Qian Ding; Yan Sun; Junliang Shang; Yuanyuan Zhang 008; Feng Li 033; Jin-Xing Liu 001 (IDMB, 2019)

NIPMI: A Network Method Based on Interaction Part Mutual Information to Detect Characteristic Genes From Integrated Data on Multi-Cancers. - Qian Ding; Junliang Shang; Yan Sun; Guangshuai Liu; Feng Li 033; Xiguo Yuan; Jin-Xing Liu 001 (IEEE Access, 2019)

IDSSIM: an lncRNA functional similarity calculation model based on an improved disease semantic similarity method. - Wenwen Fan; Junliang Shang; Feng Li 033; Yan Sun; Shasha Yuan; Jin-Xing Liu 001 (BMC Bioinform., 2020)

Detection of Driver Modules with Rarely Mutated Genes in Cancers. - Feng Li 033; Lin Gao 006; Bingbo Wang (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Multiscale part mutual information for quantifying nonlinear direct associations in networks. - Junliang Shang; Jing Wang; Yan Sun; Feng Li 033; Jin-Xing Liu 001; Honghai Zhang (Bioinform., 2021)

DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization. - Jin-Xing Liu 001; Ming-Ming Gao; Zhen Cui; Ying-Lian Gao; Feng Li 033 (BMC Bioinform., 2021)

MOPIO: A Multi-Objective Pigeon-Inspired Optimization Algorithm for Community Detection. - Junliang Shang; Yiting Li; Yan Sun; Feng Li 033; Yuanyuan Zhang 008; Jin-Xing Liu 001 (Symmetry, 2021)

scSASSL: Self-attention semi-supervised learning with deep generative models to automatically identify cell types. - Hongyu Duan; Feng Li 033; Xin Chu; Zhensheng Sun; Junliang Shang; Xikui Liu 001; Yan Li 041 (BIBM, 2022)

Probability Connectivity-Based Multimodality Regression Analysis for Associating Disease-Specific Multimodal Brain Imaging Phenotypes with Genetic Risk Factors. - Cui-Na Jiao; Chun-Hou Zheng 001; Jin-Xing Liu 001; Feng Li 033 (BIBM, 2022)

Artificial bee colony algorithm based on self-adjusting random grouping for high-order epistasis detection. - Junliang Shang; Yijun Gu; Yan Sun; Feng Li 033; Jin-Xin Liu 001; Boxin Guan (BIBM, 2022)

Identification of cancer driver modules by combining network functional and topology information. - Xin Chu; Feng Li 033; Hongyu Duan; Junliang Shang; Juan Wang 003; Jin-Xing Liu 001 (BIBM, 2022)

Construction of Gene Network Based on Inter-tumor Heterogeneity for Tumor Type Identification. - Zhensheng Sun; Junliang Shang; Hongyu Duan; Jin-Xing Liu 001; Xikui Liu 001; Yan Li 041; Feng Li 033 (ICIC (2), 2022)

A Network-Based Voting Method for Identification and Prioritization of Personalized Cancer Driver Genes. - Han Li; Feng Li 033; Junliang Shang; Xikui Liu 001; Yan Li 041 (ISBRA, 2022)

TDCOSR: A Multimodality Fusion Framework for Association Analysis Between Genes and ROIs of Alzheimer's Disease. - Qi Zou 003; Yan Sun; Feng Li 033; Juan Wang 003; Jin-Xing Liu 001; Junliang Shang (ISBRA, 2022)

idenLD-AREL: identifying lncRNA-disease associations by random forests based on an ensemble learning framework. - Yahan Li; Mingrui Zhang; Junliang Shang; Yaxuan Zhang; Feng Li 033; Jin-Xing Liu 001 (BIBM, 2023)

MKGSAGE: A Computational Framework via Multiple Kernel Fusion on GraphSAGE for Inferring Potential Disease-Related Microbes. - Shuang Wang; Jin-Xing Liu 001; Bao-Min Liu; Ling-Yun Dai; Feng Li 033; Ying-Lian Gao (BIBM, 2023)

Spectral clustering based on multi-similarity learning method for single-cell RNA-seq data. - Lianlian Zhang; Shaoyi Liu; Qianqian Ren; Junliang Shang; Xiangzhen Kong; Feng Li 033 (BIBM, 2023)

Spectral Clustering of Single-Cell RNA-Sequencing Data by Multiple Feature Sets Affinity. - Yang Liu; Feng Li 033; Junliang Shang; Daohui Ge; Qianqian Ren; Shengjun Li (ICIC (3), 2023)

scGASI: A Graph Autoencoder-Based Single-Cell Integration Clustering Method. - Tian-Jing Qiao; Feng Li 033; Shasha Yuan; Ling-Yun Dai; Juan Wang 003 (ISBRA, 2023)

ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection. - Qianqian Ren; Yahan Li; Feng Li 033; Jin-Xing Liu 001; Junliang Shang (ISBRA, 2023)

DM-MOGA: a multi-objective optimization genetic algorithm for identifying disease modules of non-small cell lung cancer. - Junliang Shang; Xuhui Zhu; Yan Sun; Feng Li 033; Xiangzhen Kong; Jin-Xing Liu 001 (BMC Bioinform., 2023)

GCCN: Graph Capsule Convolutional Network for Progressive Mild Cognitive Impairment Prediction and Pathogenesis Identification Based on Imaging Genetic Data. - Junliang Shang; Qi Zou 003; Qianqian Ren; Boxin Guan; Feng Li 033; Jin-Xing Liu 001; Yan Sun (IEEE J. Biomed. Health Informatics, 2023)

MSGCA: Drug-Disease Associations Prediction Based on Multi-Similarities Graph Convolutional Autoencoder. - Ying Wang 143; Ying-Lian Gao; Juan Wang 003; Feng Li 033; Jin-Xing Liu 001 (IEEE J. Biomed. Health Informatics, 2023)

NLRRC: A Novel Clustering Method of Jointing Non-Negative LRR and Random Walk Graph Regularized NMF for Single-Cell Type Identification. - Juan Wang 003; Lin-Ping Wang; Shasha Yuan; Feng Li 033; Jin-Xing Liu 001; Junliang Shang (IEEE J. Biomed. Health Informatics, 2023)

A multi-objective genetic algorithm based on neighborhood coevolution for community detection. - Mingyuan Bi; Junliang Shang; Xiaotong Kong; Feng Li 033; Yuanyuan Zhang 008; Jin-Xing Liu 001 (BIBM, 2024)

Spatial domains identification based on multi-view contrastive learning in spatial transcriptomics. - Yanru Gao; Feng Li 033; Fanhao Meng; Daohui Ge; Qianqian Ren; Junliang Shang (BIBM, 2024)

Integrating Autoencoder and Multi-View Graph Convolutional Networks for Spatial Domains Identification. - Fanhao Meng; Feng Li 033; Yanru Gao; Daohui Ge; Rong Zhu; Junliang Shang (BIBM, 2024)

Multi-Population Ant Colony Optimization With Knowledge-Based Local Searches for Epistasis Detection. - Qianqian Ren; Shaoyi Liu; Lianlian Zhang; Junliang Shang; Feng Li 033 (BIBM, 2024)

SGEGCAE: A Sparse Gating Enhanced Graph Convolutional Autoencoder for Multi-omics Data Integration and Classification. - Junliang Shang; Limin Zhang; Linqian Zhao; Xin He; Yan Zhao; Daohui Ge; Jin-Xing Liu 001; Feng Li 033 (ICIC (LNBI 1), 2024)

CPSORCL: A Cooperative Particle Swarm Optimization Method with Random Contrastive Learning for Interactive Feature Selection. - Junliang Shang; Yahan Li; Xiaohan Zhang; Feng Li 033; Yuanyuan Zhang 008; Jin-Xing Liu 001 (ISBRA (2), 2024)

A framework for scRNA-seq data clustering based on multi-view feature integration. - Feng Li 033; Yang Liu; Jinxing Liu 001; Daohui Ge; Junliang Shang (Biomed. Signal Process. Control., 2024)

A review of recent advances in spatially resolved transcriptomics data analysis. - Yue Gao; Ying-Lian Gao; Jing Jing 001; Feng Li 033; Chun-Hou Zheng 001; Jin-Xing Liu 001 (Neurocomputing, 2024)

A Fusion Learning Model Based on Deep Learning for Single-Cell RNA Sequencing Data Clustering. - Tian-Jing Qiao; Feng Li 033; Shasha Yuan; Ling-Yun Dai; Juan Wang 003 (J. Comput. Biol., 2024)

A feature extraction framework for discovering pan-cancer driver genes based on multi-omics data. - Xiaomeng Xue; Feng Li 033; Junliang Shang; Lingyun Dai; Daohui Ge; Qianqian Ren (Quant. Biol., 2024)

SLGCN: Structure-enhanced line graph convolutional network for predicting drug-disease associations. - Bao-Min Liu; Ying-Lian Gao; Feng Li 033; Chun-Hou Zheng 001; Jin-Xing Liu 001 (Knowl. Based Syst., 2024)

Diagnosis-Guided Deep Subspace Clustering Association Study for Pathogenetic Markers Identification of Alzheimer's Disease Based on Comparative Atlases. - Cui-Na Jiao; Junliang Shang; Feng Li 033; Xinchun Cui; Yan-Li Wang; Ying-Lian Gao; Jin-Xing Liu 001 (IEEE J. Biomed. Health Informatics, 2024)

KFDAE: CircRNA-Disease Associations Prediction Based on Kernel Fusion and Deep Auto-Encoder. - Wen-Yue Kang; Ying-Lian Gao; Ying Wang 143; Feng Li 033; Jin-Xing Liu 001 (IEEE J. Biomed. Health Informatics, 2024)

FSCME: A Feature Selection Method Combining Copula Correlation and Maximal Information Coefficient by Entropy Weights. - Qi Zhong; Junliang Shang; Qianqian Ren; Feng Li 033; Cui-Na Jiao; Jin-Xing Liu 001 (IEEE J. Biomed. Health Informatics, 2024)

M3HOGAT: A Multi-View Multi-Modal Multi-Scale High-Order Graph Attention Network for Microbe-Disease Association Prediction. - Shuang Wang; Jin-Xing Liu 001; Feng Li 033; Juan Wang 003; Ying-Lian Gao (IEEE J. Biomed. Health Informatics, 2024)

SGFCCDA: Scale Graph Convolutional Networks and Feature Convolution for circRNA-Disease Association Prediction. - Junliang Shang; Linqian Zhao; Xin He; Xianghan Meng; Limin Zhang; Daohui Ge; Feng Li 033; Jin-Xing Liu 001 (IEEE J. Biomed. Health Informatics, 2024)

MGCNRF: Prediction of Disease-Related miRNAs Based on Multiple Graph Convolutional Networks and Random Forest. - Yi Yang; Yan Sun; Feng Li 033; Boxin Guan; Jin-Xing Liu 001; Junliang Shang (IEEE Trans. Neural Networks Learn. Syst., 2024)

Predicting Potential Associations Between Microbes and Diseases Using Graph Attention Auto-encoder and PU Learning. - Jie Zheng; Lingyun Dai; Feng Li 033; Rong Zhu (ICIC (27), 2025)

Label-Guided Graph Contrastive Learning for Single-Cell Fusion Clustering. - Baojuan Qin; Junliang Shang; Yan Zhao; Xiaohan Zhang; Feng Li 033; Jin-Xing Liu 001 (ISBRA (1), 2025)

A Neighborhood Selection Learning Artificial Bee Colony Algorithm Based on Population Backtracking for Detecting Epistatic Interactions. - Yan Sun; Xiaoqi Tang; Linqian Zhao; Yaxuan Zhang; Junliang Shang; Feng Li 033; Jin-Xing Liu 001 (ISBRA (1), 2025)

SUIFS: A Symmetric Uncertainty Based Interactive Feature Selection Method. - Yan Sun; Xiaohan Zhang; Qi Zhong; Junliang Shang; Qianqian Ren; Feng Li 033; Jin-Xing Liu (ISBRA (1), 2025)

PDA-GTGCN: Identification of PiRNA-Disease Associations Based on Group Feature Transformation Graph Convolutional Network. - Xiaoqi Tang; Xianghan Meng; Junliang Shang; Baojuan Qin; Xin He; Yan Zhao; Daohui Ge; Feng Li 033; Jin-Xing Liu (ISBRA (1), 2025)

Multi-Affinity network integration based on multi-omics data for tumor stratification. - Feng Li 033; Yanru Gao; Zhensheng Sun; Shengjun Li; Junliang Shang; Jin-Xing Liu (Biomed. Signal Process. Control., 2025)

stDGAC: A novel identifying spatial domains method via graph attention contrastive network for spatial transcriptomics data. - Jing Jing 001; Yue Gao; Ying-Lian Gao; Feng Li 033; Juan Wang 003; Jin-Xing Liu 001 (Comput. Biol. Medicine, 2025)

STDDAE: Identifying spatial domains in spatial transcriptomics by dual denoising autoencoder with attention mechanism. - Yue Gao; Ying-Lian Gao; Cui-Na Jiao; Xu-Ran Dou; Feng Li 033; Jin-Xin Liu 001 (Eng. Appl. Artif. Intell., 2025)

stMHCG: High-confidence multi-view clustering for identification of spatial domains from spatially resolved transcriptomics. - Xiaohan Zhang; Junliang Shang; Yan Zhao; Baojuan Qin; Qianqian Ren; Feng Li 033; Jin-Xing Liu 001 (Neurocomputing, 2025)

A Modified Transformer Network for Seizure Detection Using EEG Signals. - Wenrong Hu; Juan Wang 003; Feng Li 033; Daohui Ge; Yuxia Wang; Qingwei Jia; Shasha Yuan (Int. J. Neural Syst., 2025)