Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. - Wei Peng 004; Jianxin Wang 001; Weiping Wang 003; Qing Liu 003; Fang-Xiang Wu; Yi Pan 001 (BMC Syst. Biol., 2012)

A dividing-and-matching algorithm to detect conserved protein complexes via local network alignment. - Wei Peng 004; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2013)

Identifying essential proteins based on protein domains in protein-protein interaction networks. - Jianxin Wang 001; Wei Peng 004; Yingjiao Chen; Yu Lu; Yi Pan 001 (BIBM, 2013)

Improving protein function prediction using domain and protein complexes in PPI networks. - Wei Peng 004; Jianxin Wang 001; Juan Cai; Lu Chen; Min Li 007; Fang-Xiang Wu (BMC Syst. Biol., 2014)

Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison. - Wei Peng 004; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (Algorithms Mol. Biol., 2015)

UDoNC: An Algorithm for Identifying Essential Proteins Based on Protein Domains and Protein-Protein Interaction Networks. - Wei Peng 004; Jianxin Wang 001; Yingjiao Cheng; Yu Lu; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure. - Wei Peng 004; Jianxin Wang 001; Bihai Zhao; Lusheng Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Predicting microRNA-disease associations by walking on four biological networks. - Wei Peng 004; Wei Lan; Jianxin Wang 001; Yi Pan 001 (BIBM, 2016)

Predicting MicroRNA-Disease Associations by Random Walking on Multiple Networks. - Wei Peng 004; Wei Lan; Zeng Yu 001; Jianxin Wang 001; Yi Pan 001 (ISBRA, 2016)

Protein-protein interactions: detection, reliability assessment and applications. - Xiaoqing Peng; Jianxin Wang 001; Wei Peng 004; Fang-Xiang Wu; Yi Pan 001 (Briefings Bioinform., 2017)

Iteration method for detecting disease genes in terms of the integration of the cellular compartment information with the protein-protein interaction data. - Xiwei Tang; Wei Peng 004; Minzhu Xie (Int. J. Data Min. Bioinform., 2017)

Predicting Protein Functions by Using Unbalanced Random Walk Algorithm on Three Biological Networks. - Wei Peng 004; Min Li 007; Lu Chen; Lusheng Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Predicting protein functions through non-negative matrix factorization regularized by protein-protein interaction network and gene functional information. - Wei Peng 004; Lun Li; Wei Dai 012; Jielin Du; Wei Lan (BIBM, 2019)

Identifying Human Essential Genes by Network Embedding Protein-Protein Interaction Network. - Wei Dai 012; Qi Chang; Wei Peng 004; Jiancheng Zhong; Yongjiang Li (ISBRA, 2019)

Improving Identification of Essential Proteins by a Novel Ensemble Method. - Wei Dai 012; Xia Li 004; Wei Peng 004; Jurong Song; Jiancheng Zhong; Jianxin Wang 001 (ISBRA, 2019)

A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph. - Junrong Song; Wei Peng 004; Feng Wang (BMC Bioinform., 2019)

A multi-view approach for predicting microbedisease associations by fusing the linear and nonlinear features. - Ming Liu; Wei Dai 012; Wei Peng 004; Yu Fu; Yi Pan 001 (BIBM, 2020)

Inferring LncRNA-disease associations based on graph autoencoder matrix completion. - Ximin Wu; Wei Lan; Qingfeng Chen; Yi Dong; Jin Liu 012; Wei Peng 004 (Comput. Biol. Chem., 2020)

Predicting protein functions by using non-negative matrix factorisation with multi-networks co-regularisation. - Wei Peng 004; Jielin Du; Lun Li; Wei Dai 012; Wei Lan (Int. J. Data Min. Bioinform., 2020)

An Entropy-Based Method for Identifying Mutual Exclusive Driver Genes in Cancer. - Junrong Song; Wei Peng 004; Feng Wang (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

A Heterogeneous Graph Convolutional Network-Based Deep Learning Model to Identify miRNA-Disease Association. - Zicheng Che; Wei Peng 004; Wei Dai 012; Shoulin Wei; Wei Lan (ISBRA, 2021)

Proteoform characterization based on top-down mass spectrometry. - Jiancheng Zhong; Yusui Sun; Minzhu Xie; Wei Peng 004; Chushu Zhang; Fang-Xiang Wu; Jianxin Wang 001 (Briefings Bioinform., 2021)

A novel essential protein identification method based on PPI networks and gene expression data. - Jiancheng Zhong; Chao Tang; Wei Peng 004; Minzhu Xie; Yusui Sun; Qiang Tang; Qiu Xiao; Jiahong Yang (BMC Bioinform., 2021)

Prediction of circRNA-miRNA Associations Based on Network Embedding. - Wei Lan; Mingrui Zhu; Qingfeng Chen; Jianwei Chen; Jin Ye 003; Jin Liu 012; Wei Peng 004; Shirui Pan (Complex., 2021)

A Novel Multi-Ensemble Method for Identifying Essential Proteins. - Wei Dai 012; Bingxi Chen; Wei Peng 004; Xia Li 004; Jiancheng Zhong; Jianxin Wang 001 (J. Comput. Biol., 2021)

Identification of personalized driver genes for individuals using graph convolution network. - Wei Peng 004; Piaofang Yu; Wei Dai 012; Xiaodong Fu; Li Liu 032; Yi Pan 001 (BIBM, 2022)

Collusion Attack Analysis and Detection of DPoS Consensus Mechanism. - Xinxin Qi; Xiaodong Fu; Fei Dai 002; Li Liu 032; Lijun Liu; Jiaman Ding; Wei Peng 004 (BlockSys, 2022)

Improving cancer driver gene identification using multi-task learning on graph convolutional network. - Wei Peng 004; Qi Tang; Wei Dai 012; Tielin Chen (Briefings Bioinform., 2022)

Predicting cancer drug response using parallel heterogeneous graph convolutional networks with neighborhood interactions. - Wei Peng 004; Hancheng Liu; Wei Dai 012; Ning Yu 004; Jianxin Wang 001 (Bioinform., 2022)

GANLDA: Graph attention network for lncRNA-disease associations prediction. - Wei Lan; Ximin Wu; Qingfeng Chen; Wei Peng 004; Jianxin Wang 001; Yi-Ping Phoebe Chen (Neurocomputing, 2022)

Identifying Cancer Patient Subgroups by Finding Co-Modules From the Driver Mutation Profiles and Downstream Gene Expression Profiles. - Junrong Song; Wei Peng 004; Feng Wang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Predicting Drug Response Based on Multi-Omics Fusion and Graph Convolution. - Wei Peng 004; Tielin Chen; Wei Dai 012 (IEEE J. Biomed. Health Informatics, 2022)

Essential proteins identification based on weak consensus model and neighborhood aggregation centrality. - Zhipeng Hu; Gaoshi Li; Jingli Wu; Xinlong Luo 002; Jiafei Liu; Wei Peng 004; Xiaoshu Zhu (BIBM, 2023)

A multi-view comparative learning method for spatial transcriptomics data clustering. - Wei Peng 004; Zhihao Zhang; Wei Dai 012; Xiaodong Fu; Li Liu 032; Lijun Liu; Ning Yu 004 (BIBM, 2023)

Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model. - Wei Peng 004; Zicheng Che; Wei Dai 012; Shoulin Wei; Wei Lan (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Multi-View Feature Aggregation for Predicting Microbe-Disease Association. - Wei Peng 004; Ming Liu; Wei Dai 012; Tielin Chen; Yu Fu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

RA-DENet: Reverse Attention and Distractions Elimination Network for polyp segmentation. - Kaiqi Wang; Li Liu 032; Xiaodong Fu; Lijun Liu; Wei Peng 004 (Comput. Biol. Medicine, 2023)

Improving drug response prediction based on two-space graph convolution. - Wei Peng 004; Tielin Chen; Hancheng Liu; Wei Dai 012; Ning Yu 004; Wei Lan (Comput. Biol. Medicine, 2023)

Crowded pose-guided multi-task learning for instance-level human parsing. - Yong Wei; Li Liu 032; Xiaodong Fu; Lijun Liu; Wei Peng 004 (Mach. Vis. Appl., 2023)

Feature Representation for High-resolution Clothed Human Reconstruction. - Juncheng Pu; Li Liu 032; Xiaodong Fu; Zhuo Su 001; Lijun Liu; Wei Peng 004 (Comput. Graph. Forum, 2023)

Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism. - Wei Peng 004; Rong Wu; Wei Dai 012; Ning Yu 004 (BMC Bioinform., 2023)

Essential proteins discovery based on dominance relationship and neighborhood similarity centrality. - Gaoshi Li; Xinlong Luo 002; Zhipeng Hu; Jingli Wu; Wei Peng 004; Jiafei Liu; Xiaoshu Zhu (Health Inf. Sci. Syst., 2023)

Sparse Attention-based Hierarchical Node Representation for Spatial Domain Identification. - Wei Peng 004; Zhihao Ping; Wei Dai 012; Xiaodong Fu; Li Liu 032; Lijun Liu; Ning Yu 004 (BIBM, 2024)

Patient Anticancer Drug Response Prediction Based on Single-Cell Deconvolution. - Wei Peng 004; Chuyue Chen; Wei Dai 012 (ISBRA (3), 2024)

Hypergraph Representation Learning for Cancer Drug Response Prediction. - Wei Peng 004; Jiangzhen Lin; Wei Dai 012; Gong Chen; Xiaodong Fu; Li Liu 032; Lijun Liu (ISBRA (2), 2024)

DGCL: A Contrastive Learning Method for Predicting Cancer Driver Genes Based on Graph Diffusion. - Wei Peng 004; Zhengnan Zhou; Wei Dai 012; Xinping Xu; Xiaodong Fu; Li Liu 032; Lijun Liu (ISBRA (2), 2024)

Transformer-Based Single-Cell Language Model: A Survey. - Wei Lan; Guohang He; Mingyang Liu; Qingfeng Chen; Junyue Cao; Wei Peng 004 (Big Data Min. Anal., 2024)

Identification of Cancer Driver Genes based on Dynamic Incentive Model. - Zhipeng Hu; Gaoshi Li; Xinlong Luo 002; Wei Peng 004; Jiafei Liu; Xiaoshu Zhu; Jingli Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Multi-Network Graph Contrastive Learning for Cancer Driver Gene Identification. - Wei Peng 004; Zhengnan Zhou; Wei Dai 012; Ning Yu 004; Jianxin Wang 001 (IEEE Trans. Netw. Sci. Eng., 2024)

Supervised graph contrastive learning for cancer subtype identification through multi-omics data integration. - Fangxu Chen; Wei Peng 004; Wei Dai 012; Shoulin Wei; Xiaodong Fu; Li Liu 032; Lijun Liu (Health Inf. Sci. Syst., 2024)

Identification of cancer driver genes based on hierarchical weak consensus model. - Gaoshi Li; Zhipeng Hu; Xinlong Luo 002; Jiafei Liu; Jingli Wu; Wei Peng 004; Xiaoshu Zhu (Health Inf. Sci. Syst., 2024)

A Survival Prediction Model Integrating Hierarchical Pathological Image and Pathway Features. - Xinyue Xu; Wei Peng 004; Wei Dai 012; Xiaodong Fu; Li Liu 032; Lijun Liu (ISBRA (2), 2025)

Multi-domains personalized local differential privacy frequency estimation mechanism for utility optimization. - Yunfei Li; Xiaodong Fu; Li Liu 032; Jiaman Ding; Wei Peng 004; Lianyin Jia (Comput. Secur., 2025)

Fusion of brain imaging genetic data for alzheimer's disease diagnosis and causal factors identification using multi-stream attention mechanisms and graph convolutional networks. - Wei Peng 004; Yanhan Ma; Chunshan Li; Wei Dai 012; Xiaodong Fu; Li Liu 032; Lijun Liu; Jin Liu 012 (Neural Networks, 2025)

Predicting Clinical Anticancer Drug Response of Patients by Using Domain Alignment and Prototypical Learning. - Wei Peng 004; Chuyue Chen; Wei Dai 012; Ning Yu 004; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2025)

The Large Language Models on Biomedical Data Analysis: A Survey. - Wei Lan; Zhentao Tang; Mingyang Liu; Qingfeng Chen; Wei Peng 004; Yi-Ping Phoebe Chen; Yi Pan 001 (IEEE J. Biomed. Health Informatics, 2025)

Redefining medical visual question answering using conditional generative diffusion models. - Bing Liu; Lijun Liu; Xiaobing Yang; Wei Peng 004; Li Liu 032 (Biomed. Signal Process. Control., 2026)