Revealing protein functions based on relationships of interacting proteins and GO terms. - Zhixia Teng; Maozu Guo 001; Xiaoyan Liu; Zhen Tian 004; Kai Che (BIBM, 2016)

Constructing an integrated gene similarity network for the identification of disease genes. - Zhen Tian 004; Maozu Guo 001; Chunyu Wang 002; Linlin Xing; Lei Wang 085; Yin Zhang 009 (BIBM, 2016)

SGFSC: speeding the gene functional similarity calculation based on hash tables. - Zhen Tian 004; Chunyu Wang 002; Maozu Guo 001; Xiaoyan Liu; Zhixia Teng (BMC Bioinform., 2016)

An improved method for functional similarity analysis of genes based on Gene Ontology. - Zhen Tian 004; Chunyu Wang 002; Maozu Guo 001; Xiaoyan Liu; Zhixia Teng (BMC Syst. Biol., 2016)

Refine gene functional similarity network based on interaction networks. - Zhen Tian 004; Maozu Guo 001; Chunyu Wang 002; Xiaoyan Liu; Shiming Wang (BMC Bioinform., 2017)

Computational drug repositioning using meta-path-based semantic network analysis. - Zhen Tian 004; Zhixia Teng; Shuang Cheng; Maozu Guo 001 (BMC Syst. Biol., 2018)

A Stacked Ensemble Learning Framework with Heterogeneous Feature Combinations for Predicting ncRNA-Protein Interaction. - Qiguo Dai; Zhaowei Wang 005; Jinmiao Song; Xiaodong Duan; Maozu Guo 001; Zhen Tian 004 (BIBM, 2020)

SWE: a novel method with semantic-weighted edge for measuring gene functional similarity. - Zhen Tian 004; Haichuan Fang; Yangdong Ye; Zhenfeng Zhu (BIBM, 2020)

ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition. - Zhixia Teng; Zitong Zhang 002; Zhen Tian 004; Yanjuan Li; Guohua Wang 001 (BMC Bioinform., 2021)

Predicting miRNA-disease associations via learning multimodal networks and fusing mixed neighborhood information. - Zhengzheng Lou; Zhaoxu Cheng; Hui Li; Zhixia Teng; Yang Liu; Zhen Tian 004 (Briefings Bioinform., 2022)

MHADTI: predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms. - Zhen Tian 004; Xiangyu Peng; Haichuan Fang; Wenjie Zhang 008; Qiguo Dai; Yangdong Ye (Briefings Bioinform., 2022)

A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. - Zhen Tian 004; Haichuan Fang; Yangdong Ye; Zhenfeng Zhu (BMC Bioinform., 2022)

Learning knowledge graph embedding with a dual-attention embedding network. - Haichuan Fang; Youwei Wang; Zhen Tian 004; Yangdong Ye (Expert Syst. Appl., 2023)

GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes. - Zhen Tian 004; Haichuan Fang; Zhixia Teng; Yangdong Ye (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Predicting microbe-drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy. - Zhen Tian 004; Yue Yu; Haichuan Fang; Weixin Xie; Maozu Guo 001 (Briefings Bioinform., 2023)

Drug-target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism. - Wei Song; Lewen Xu; Chenguang Han; Zhen Tian 004; Quan Zou 001 (Bioinform., 2024)

MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy. - Zhen Tian 004; Chenguang Han; Lewen Xu; Zhixia Teng; Wei Song (Briefings Bioinform., 2024)

Clustering scRNA-seq data with the cross-view collaborative information fusion strategy. - Zhengzheng Lou; Xiaojiao Wei; Yuanhao Hu; Shizhe Hu; Yucong Wu; Zhen Tian 004 (Briefings Bioinform., 2024)

EchoDiffusion: Waveform Conditioned Diffusion Models for Echo-Based Depth Estimation. - Wenjie Zhang 008; Jun Yin; Long Ma; Peng Yu; Xiaoheng Jiang; Zhen Tian 004; Mingliang Xu 001 (AAAI, 2025)

Drug-Target Interaction Prediction with Pretrained LLM Feature Learning and Cross-Modal Fusion Strategy. - Rongqi Fan; Zhiyuan Dong; Zhen Tian 004; Pengyuan Li 014; Yufeng Ling; Haoran Zhu; Wei Song (BIBM, 2025)

CDIB: Consistency Discovery-guided Information Bottleneck for Multi-modal Knowledge Graph Reasoning. - Haichuan Fang; Haoran Zhang; Yulin Du; Qiang Guo 012; Zhen Tian 004; Youwei Wang; Yangdong Ye (ACM Multimedia, 2025)

Differentiable graph clustering with structural grouping for single-cell RNA-seq data. - Xiaoqiang Yan; Shike Du; Quan Zou 001; Zhen Tian 004 (Bioinform., 2025)

Hierarchical feature aggregation with mixed attention mechanism for single-cell RNA-seq analysis. - Wanning Zhou; Wei Song; Zhuangzhuang Zhang; Fan Zhang; Zhixia Teng; Zhen Tian 004 (Expert Syst. Appl., 2025)

Drug repositioning by collaborative learning based on graph convolutional inductive network. - Zhixia Teng; Yongliang Li; Zhen Tian 004; Yingjian Liang; Guohua Wang 001 (Future Gener. Comput. Syst., 2025)

Few-Shot Object Counting with frequency attention and multi-perception head. - Gaoxin Ma; Xingquan Zhu 001; Zhen Tian 004; Yangdong Ye; Zhenfeng Zhu (Neurocomputing, 2025)

Decoupled contrastive multi-view clustering with adaptive false negative elimination for cancer subtyping. - Mengxiang Lin; Rongqi Fan; Saisai Zhu; Xiaoqiang Yan; Quan Zou 001; Zhen Tian 004 (PLoS Comput. Biol., 2025)

DSANIB: Drug-Target Interaction Predictions With Dual-View Synergistic Attention Network and Information Bottleneck Strategy. - Zhen Tian 004; Zhuangzhuang Zhang; Wanning Zhou; Zhixia Teng; Wei Song; Quan Zou 001 (IEEE J. Biomed. Health Informatics, 2025)

HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction. - Yuguang Li; Zhen Tian 004; Xiaofei Nan; Shoutao Zhang; Qinglei Zhou; Shuai Lu (Briefings Bioinform., 2025)

MAEST: accurately spatial domain detection in spatial transcriptomics with graph masked autoencoder. - Pengfei Zhu; Han Shu; Yongtian Wang; Xiaofeng Wang; Yuan Zhao; Jialu Hu; Jiajie Peng; Xuequn Shang 001; Zhen Tian 004; Jing Chen; Tao Wang 082 (Briefings Bioinform., 2025)

Enhancing LncRNA-miRNA interaction prediction with multimodal contrastive representation learning. - Zhixia Teng; Zhaowen Tian; Murong Zhou; Guohua Wang 001; Zhen Tian 004; Yuming Zhao (Briefings Bioinform., 2025)

Self-Cumulative Contrastive Graph Clustering. - Xiaoqiang Yan; Kun Deng; Quan Zou 001; Zhen Tian 004; Hui Yu 001 (IEEE CAA J. Autom. Sinica, 2025)

Adaptive multi-view information bottleneck for multi-omics data clustering. - Zhen Tian 004; Xiaojiao Wei; Zhengzheng Lou; Zhixia Teng; Shouli Fu (Briefings Bioinform., 2026)

MFCLDTA: Multi-scale feature contrastive learning for predicting drug-target binding affinity. - Zhen Tian 004; Saisai Zhu; Zhixia Teng; Xiaoqiang Yan; Tao Wang 082 (Expert Syst. Appl., 2026)

A Stitch in Time Saves Nine: Progressive Information Bottleneck for Incremental Multiview Clustering. - Xiaoqiang Yan; Fengshou Han; Yiqiao Mao; Zhen Tian 004; Witold Pedrycz; Hui Yu 001 (IEEE Trans. Comput. Soc. Syst., 2026)

Contrastive Variational Graph Symmetric Autoencoder for Full Extrapolation Over Temporal Knowledge Graphs. - Haichuan Fang; Zhen Tian 004; Youwei Wang; Bo Ji; Yangdong Ye (IEEE Trans. Syst. Man Cybern. Syst., 2026)