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)

PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data. - Shudong Wang; Lihua Wang; Yuanyuan Zhang 008; Shanchen Pang; Xinzeng Wang (BMC Bioinform., 2019)

Identification of PIWI-interacting RNA modules by weighted correlation network analysis. - Yajun Liu; Junying Zhang; Aimin Li; Yuanyuan Zhang 008; Yaoyao Li; Xiguo Yuan; Zhongzhen He; Zhaowen Liu; Shouheng Tuo (Clust. Comput., 2019)

SINE: Second-Order Information Network Embedding. - Ziqi Wang; Yuanyuan Zhang 008; Shudong Wang; Junliang Shang (IEEE Access, 2020)

PESM: A novel approach of tumor purity estimation based on sample specific methylation sites. - Shanchen Pang; Lihua Wang; Shudong Wang; Yuanyuan Zhang 008; Xinzeng Wang (J. Bioinform. Comput. Biol., 2020)

Identification of Critical Core Genes of Sarcoma Based on Centrality Analysis of Networks Nodes. - Shudong Wang; Jixiao Wang; Xinzeng Wang; Yuanyuan Zhang 008; Tao Yi (J. Medical Imaging Health Informatics, 2020)

HGDD: A Drug-Disease High-Order Association Information Extraction Method for Drug Repurposing via Hypergraph. - Shanchen Pang; Kuijie Zhang; Shudong Wang; Yuanyuan Zhang 008; Sicheng He; Wenhao Wu; Sibo Qiao (ISBRA, 2021)

TagSNP-set selection for genotyping using integrated data. - Shudong Wang; Gaowei Liu; Xinzeng Wang; Yuanyuan Zhang 008; Sicheng He; Yulin Zhang (Future Gener. Comput. Syst., 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)

AF-GCN: Completing various graph tasks efficiently via adaptive quadratic frequency response function in graph spectral domain. - Shanchen Pang; Kuijie Zhang; Gan Wang; Jerry Chun-Wei Lin; Fuyu Wang; Xiangyu Meng; Shudong Wang; Yuanyuan Zhang 008 (Inf. Sci., 2023)

Predicting potential small molecule-miRNA associations utilizing truncated schatten p-norm. - Shudong Wang; Tiyao Liu; Chuanru Ren; Wenhao Wu; Zhiyuan Zhao 003; Shanchen Pang; Yuanyuan Zhang 008 (Briefings Bioinform., 2023)

Generative Adversarial Matrix Completion Network based on Multi-Source Data Fusion for miRNA-Disease Associations Prediction. - Shudong Wang; Yunyin Li; Yuanyuan Zhang 008; Shanchen Pang; Sibo Qiao; Yu Zhang; Fuyu Wang (Briefings Bioinform., 2023)

TranSEFusionNet: Deep fusion network for colorectal polyp segmentation. - Yuanyuan Zhang 008; Lin Liu; Ziyi Han; Fanyun Meng; Yulin Zhang; Yawu Zhao (Biomed. Signal Process. Control., 2023)

VGAEDTI: drug-target interaction prediction based on variational inference and graph autoencoder. - Yuanyuan Zhang 008; Yinfei Feng; Mengjie Wu; Zengqian Deng; Shudong Wang (BMC Bioinform., 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)

IEARACDA: Predicting circRNA-disease associations based on information enhancement and arctangent rank approximation. - Shanchen Pang; Zheqi Song; Tiyao Liu; Wenhao Wu; Yuanyuan Zhang 008; Shudong Wang (BIBM, 2024)

A Particle Swarm Optimization Algorithm Based on Multi-Population Mutual Learning for SNP-SNP Interaction Detection. - Linqian Zhao; Yahan Li; Junliang Shang; Qianqian Ren; Yuanyuan Zhang 008; Jin-Xing Liu 001 (BIBM, 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)

Heterogeneous graph inference with range constrainted L2,1-collaborative matrix factorization for small molecule-miRNA association prediction. - Shudong Wang; Tiyao Liu; Chuanru Ren; Yawu Zhao; Sibo Qiao; Yuanyuan Zhang 008; Shanchen Pang (Comput. Biol. Chem., 2024)

Multi-resolution sequence and structure feature extraction for binding site prediction. - Wenjing Yin; Shudong Wang; Sibo Qiao; Yuanyuan Zhang 008; Shanchen Pang (Eng. Appl. Artif. Intell., 2024)

DeFuseDTI: Interpretable drug target interaction prediction model with dual-branch encoder and multiview fusion. - Baoming Feng; Yuan-Yuan Zhang 008; Niu-Wang-Jie Niu; Hao-Yu Zheng; Jin-Long Wang 002; Wen-Feng Feng (Future Gener. Comput. Syst., 2024)

MolLoG: A Molecular Level Interpretability Model Bridging Local to Global for Predicting Drug Target Interactions. - Baoming Feng; Yuan-Yuan Zhang 008; Xiaochen Zhou; Jin-Long Wang 002; Yinfei Feng (J. Chem. Inf. Model., 2024)

TIWMFLP: Two-Tier Interactive Weighted Matrix Factorization and Label Propagation Based on Similarity Matrix Fusion for Drug-Disease Association Prediction. - Tiyao Liu; Shudong Wang; Yuanyuan Zhang 008; Yunyin Li; Yingye Liu; Shiyuan Huang (J. Chem. Inf. Model., 2024)

Multirelational Hypergraph Representation Learning for Predicting circRNA-miRNA Associations. - Wenjing Yin; Shudong Wang; Yuanyuan Zhang 008; Sibo Qiao; Wenhao Wu; Hengxiao Li (J. Chem. Inf. Model., 2024)

Application of Artificial Intelligence in Drug-Drug Interactions Prediction: A Review. - Yuanyuan Zhang 008; Zengqian Deng; Xiaoyu Xu; Yinfei Feng; Junliang Shang (J. Chem. Inf. Model., 2024)

TSCNet: Topology and semantic co-mining node representation learning based on direct perception strategy. - Kuijie Zhang; Shanchen Pang; Yuanyuan Zhang 008; Wenhao Wu; Xiao He 012; Haiyuan Gui (Knowl. Based Syst., 2024)

SimHOEPI: A resampling simulator for generating single nucleotide polymorphism data with a high-order epistasis model. - Yahan Li; Xinrui Cai; Junliang Shang; Yuanyuan Zhang 008; Jin-Xing Liu 001 (Quant. Biol., 2024)

DualA-Net: A generalizable and adaptive network with dual-branch encoder for medical image segmentation. - Yuanyuan Zhang 008; Ziyi Han; Lin Liu; Shudong Wang (Comput. Methods Programs Biomed., 2024)

Graph attention autoencoder model with dual decoder for clustering single-cell RNA sequencing data. - Shudong Wang; Yu Zhang; Yuanyuan Zhang 008; Yulin Zhang; Shanchen Pang; Jionglong Su; Yingye Liu (Appl. Intell., 2024)

MOSGAT: Uniting Specificity-Aware GATs and Cross Modal-Attention to Integrate Multi-Omics Data for Disease Diagnosis. - Wenhao Wu; Shudong Wang; Yuanyuan Zhang 008; Wenjing Yin; Yawu Zhao; Shanchen Pang (IEEE J. Biomed. Health Informatics, 2024)

Collaborative Construction Method of Biomedical Knowledge Graph Based on Multi-Blockchain. - Jinlong Wang 002; Zhenxi Xie; Hui Xin; Pengjun Li; Yuanyuan Zhang 008; Xiaoyun Xiong; Jerry Chun-Wei Lin (Distributed Ledger Technol. Res. Pract., 2024)

scSFCL:Deep clustering of scRNA-seq data with subspace feature confidence learning. - Xiaokun Meng; Yuanyuan Zhang 008; Xiaoyu Xu; Kaihao Zhang; Baoming Feng (Comput. Biol. Chem., 2025)

Dynamic scheduling in flexible and hybrid disassembly systems with manual and automated workstations using reward-shaping enhanced reinforcement learning. - Jinlong Wang 002; Qihuiyang Liang; Min Li; Zelin Qu; Yuanyuan Zhang 008 (Eng. Appl. Artif. Intell., 2025)

Risk identification of listed companies violation by integrating knowledge graph and multi-source risk factors. - Jinlong Wang 002; Pengjun Li; Yingmin Liu; Xiaoyun Xiong; Yuanyuan Zhang 008; Zhihan Lv (Eng. Appl. Artif. Intell., 2025)

Multi-echelon inventory optimization of waste electrical and electronic equipment closed-loop supply chain based on reinforcement learning under carbon tax policy. - Jinlong Wang 002; Shangzhuo Zhou; Min Li; Guanyu Ren; Xianquan Ren; Xiaoyun Xiong; Yuanyuan Zhang 008 (Eng. Appl. Artif. Intell., 2025)

Deciphering circRNA-drug sensitivity associations via global-local heterogeneous matrix factorization and hypergraph contrastive learning. - Tiyao Liu; Shudong Wang; Yuanyuan Zhang 008; Shanchen Pang; Wenjing Yin; Wenhao Wu; Yingye Liu (Expert Syst. Appl., 2025)

MOHGCN: A trustworthy multi-omics data integration framework based on specificity-aware heterogeneous graph convolutional neural networks for disease diagnosis. - Wenhao Wu; Shudong Wang; Yuanyuan Zhang 008; Kuijie Zhang; Wenjing Yin; Shanchen Pang (Expert Syst. Appl., 2025)

IRPCA: An Interpretable Robust Principal Component Analysis Framework for Inferring miRNA-Drug Associations. - Yunyin Li; Shudong Wang; Yuanyuan Zhang 008; Chuanru Ren; Tiyao Liu; Yingye Liu; Shanchen Pang (J. Chem. Inf. Model., 2025)

scMDCL: A Deep Collaborative Contrastive Learning Framework for Matched Single-Cell Multiomics Data Clustering. - Wenhao Wu; Shudong Wang; Kuijie Zhang; Hengxiao Li; Sibo Qiao; Yuanyuan Zhang 008; Shanchen Pang (J. Chem. Inf. Model., 2025)

MOCapsNet: Multiomics Data Integration for Cancer Subtype Analysis Based on Dynamic Self-Attention Learning and Capsule Networks. - Yuanyuan Zhang 008; Haoyu Zheng; Xiaokun Meng; Qihao Wang; Zimin Li; Wenhao Wu (J. Chem. Inf. Model., 2025)

Dual Encoder Cross-Shape Transformer Network for Medical Image Segmentation in Internet of Medical Things for Consumer Health. - Yawu Zhao; Shudong Wang; Yulin Zhang; Yande Ren; Yuanyuan Zhang 008; Shanchen Pang (IEEE Trans. Consumer Electron., 2025)

Convolution Bridge: An Effective Algorithmic Migration Strategy From CNNs to GNNs. - Kuijie Zhang; Shanchen Pang; Huahui Yang; Yuanyuan Zhang 008; Wenhao Wu; Hengxiao Li; Jerry Chun-Wei Lin (IEEE Trans. Neural Networks Learn. Syst., 2025)