Improved DNA-Binding Protein Identification by Incorporating Evolutionary Information Into the Chou's PseAAC. - Xiangzheng Fu; Wen Zhu; Bo Liao; Lijun Cai; Lihong Peng; Jialiang Yang (IEEE Access, 2018)

Improved Prediction of Cell-Penetrating Peptides via Effective Orchestrating Amino Acid Composition Feature Representation. - Xiangzheng Fu; Lixia Ke; Lijun Cai; Xiangtao Chen; Xuanbai Ren; Mingyu Gao 004 (IEEE Access, 2019)

StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency. - Xiangzheng Fu; Lijun Cai; Xiangxiang Zeng; Quan Zou 001 (Bioinform., 2020)

Nonnegative Matrix Factorization Framework for Disease-Related CircRNA Prediction. - Cheng Yang; Li Peng; Wei Liu 150; Xiangzheng Fu; Ni Li (ICA3PP (3), 2021)

Drug repositioning based on the heterogeneous information fusion graph convolutional network. - Lijun Cai; Changcheng Lu; Junlin Xu; Yajie Meng; Peng Wang 035; Xiangzheng Fu; Xiangxiang Zeng; Yansen Su (Briefings Bioinform., 2021)

iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor. - Lijun Cai; Xuanbai Ren; Xiangzheng Fu; Li Peng; Mingyu Gao 004; Xiangxiang Zeng (Bioinform., 2021)

ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation. - Lijun Cai; Li Wang 145; Xiangzheng Fu; Chenxing Xia; Xiangxiang Zeng; Quan Zou 001 (Briefings Bioinform., 2021)

NSCGRN: a network structure control method for gene regulatory network inference. - Wei Liu 150; Xingen Sun; Li Yang; Kaiwen Li; Yu Yang; Xiangzheng Fu (Briefings Bioinform., 2022)

DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder. - Li Peng; Yuan Tu; Li Huang; Yang Li; Xiangzheng Fu; Xiang Chen (Briefings Bioinform., 2022)

RNMFLP: Predicting circRNA-disease associations based on robust nonnegative matrix factorization and label propagation. - Li Peng; Cheng Yang; Li Huang; Xiang Chen; Xiangzheng Fu; Wei Liu 150 (Briefings Bioinform., 2022)

Predicting ncRNA-protein interactions based on dual graph convolutional network and pairwise learning. - Linlin Zhuo; Bosheng Song; Yuansheng Liu; Zejun Li; Xiangzheng Fu (Briefings Bioinform., 2022)

A dynamic population reduction differential evolution algorithm combining linear and nonlinear strategy piecewise functions. - Kangshun Li; Xiangzheng Fu; Feng Wang; Hassan Jalil (Concurr. Comput. Pract. Exp., 2022)

NSRGRN: a network structure refinement method for gene regulatory network inference. - Wei Liu 150; Yu Yang; Xu Lu 002; Xiangzheng Fu; Ruiqing Sun; Li Yang; Li Peng (Briefings Bioinform., 2023)

HeadTailTransfer: An efficient sampling method to improve the performance of graph neural network method in predicting sparse ncRNA-protein interactions. - Jinhang Wei; Linlin Zhuo; Shiyao Pan; Xinze Lian; Xiaojun Yao; Xiangzheng Fu (Comput. Biol. Medicine, 2023)

MPCLCDA: predicting circRNA-disease associations by using automatically selected meta-path and contrastive learning. - Wei Liu 150; Ting Tang; Xu Lu 002; Xiangzheng Fu; Yu Yang; Li Peng (Briefings Bioinform., 2023)

GCFMCL: predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning. - Jinhang Wei; Linlin Zhuo; Zhecheng Zhou; Xinze Lian; Xiangzheng Fu; Xiaojun Yao (Briefings Bioinform., 2023)

MHAM-NPI: Predicting ncRNA-protein interactions based on multi-head attention mechanism. - Zhecheng Zhou; Zhenya Du; Jinhang Wei; Linlin Zhuo; Shiyao Pan; Xiangzheng Fu; Xinze Lian (Comput. Biol. Medicine, 2023)

Dual-Stream Heterogeneous Graph Neural Network Based on Zero-Shot Embeddings for Predicting miRNA-Drug Sensitivity. - Li Peng; Wang Wang; Cheng Yang; Wenhui Xiao; Xiangzheng Fu; Yifan Chen (BIBM, 2024)

A Novel Approach for Subtype Identification via Multi-omics Data Using Adversarial Autoencoder. - Xia Chen; Hao Nie; Quanwei Chen; Xiang Zhang; Zixing He; Xiuxiu Chao; Weihao Ou; Xiangzheng Fu; Haowen Chen (ISBRA (1), 2024)

ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction. - Lijun Cai; Guanyu Yue; Yifan Chen; Li Wang 145; Xiaojun Yao; Quan Zou 001; Xiangzheng Fu; Dong-Sheng Cao 001 (Briefings Bioinform., 2024)

MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning. - Tao Wang; Zhen Li 015; Linlin Zhuo; Yifan Chen; Xiangzheng Fu; Quan Zou 001 (Briefings Bioinform., 2024)

Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization. - Rui Wang; Tao Wang; Linlin Zhuo; Jinhang Wei; Xiangzheng Fu; Quan Zou 001; Xiaojun Yao (Briefings Bioinform., 2024)

Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs. - Zhecheng Zhou; Linlin Zhuo; Xiangzheng Fu; Quan Zou 001 (Briefings Bioinform., 2024)

MR2CPPIS: Accurate prediction of protein-protein interaction sites based on multi-scale Res2Net with coordinate attention mechanism. - Yinyin Gong; Rui Li 019; Yan Liu 032; Jilong Wang 002; Buwen Cao; Xiangzheng Fu; Renfa Li; Danny Z. Chen (Comput. Biol. Medicine, 2024)

Advancing cancer driver gene detection via Schur complement graph augmentation and independent subspace feature extraction. - Xinqian Ma; Zhen Li 015; Zhenya Du; Yan Xu; Yifan Chen; Linlin Zhuo; Xiangzheng Fu; Ruijun Liu (Comput. Biol. Medicine, 2024)

Enhancing drug-food interaction prediction with precision representations through multilevel self-supervised learning. - Jinhang Wei; Zhen Li 015; Linlin Zhuo; Xiangzheng Fu; Mingjing Wang; Keqin Li 001; Chengshui Chen (Comput. Biol. Medicine, 2024)

HMAMP: Hypervolume-Driven Multi-Objective Antimicrobial Peptides Design. - Li Wang 145; Yiping Li; Xiangzheng Fu; Xiucai Ye; Junfeng Shi; Gary G. Yen; Xiangxiang Zeng (CoRR, 2024)

MoFormer: Multi-objective Antimicrobial Peptide Generation Based on Conditional Transformer Joint Multi-modal Fusion Descriptor. - Li Wang 145; Xiangzheng Fu; Jiahao Yang; Xinyi Zhang; Xiucai Ye; Yiping Liu; Tetsuya Sakurai; Xiangxiang Zeng (CoRR, 2024)

Multi-source data integration for explainable miRNA-driven drug discovery. - Zhen Li 015; Qingquan Liao; Wenbin Liu; Peng Xu 004; Linlin Zhuo; Xiangzheng Fu; Quan Zou 001 (Future Gener. Comput. Syst., 2024)

Developing explainable models for lncRNA-Targeted drug discovery using graph autoencoders. - Huiying Liu; Xiangzheng Fu; Haiting Chen; Jun Shang; Haoyu Zhou; Wang Zhe; Xiaojun Yao (Future Gener. Comput. Syst., 2024)

ML-NPI: Predicting Interactions between Noncoding RNA and Protein Based on Meta-Learning in a Large-Scale Dynamic Graph. - Tao Wang; Wentao Wang; Xin Jiang 006; Jiaxing Mao; Linlin Zhuo; Mingzhe Liu 001; Xiangzheng Fu; Xiaojun Yao (J. Chem. Inf. Model., 2024)

An Effective Plant Small Secretory Peptide Recognition Model Based on Feature Correction Strategy. - Rui Wang; Zhecheng Zhou; Xiaonan Wu; Xin Jiang 006; Linlin Zhuo; Mingzhe Liu 001; Hao Li 025; Xiangzheng Fu; Xiaojun Yao (J. Chem. Inf. Model., 2024)

ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification. - Tao Wang; Linlin Zhuo; Yifan Chen; Xiangzheng Fu; Xiangxiang Zeng; Quan Zou 001 (PLoS Comput. Biol., 2024)

Dual-View Learning Based on Images and Sequences for Molecular Property Prediction. - Xiang Zhang; Hongxin Xiang; Xixi Yang; Jingxin Dong 002; Xiangzheng Fu; Xiangxiang Zeng; Haowen Chen; Keqin Li 001 (IEEE J. Biomed. Health Informatics, 2024)

SGPS-IMR: Efficiently inferring microbial resistance using self-supervised graph perturbation strategy. - Wentao Wang; Linlin Zhuo; Zhecheng Zhou; Xiangzheng Fu; Quan Zou 001 (Expert Syst. Appl., 2025)

SQ-DiffuPep: A multimodal information-guided quantitative latent diffusion model for antimicrobial peptide discovery. - Luoda Tan; Li Wang 145; Xuanbai Ren; Quan Zou 001; Xiaojun Yao; Xiangxiang Zeng; Xiangzheng Fu (Inf. Fusion, 2025)

A Innovative Strategy for Identifying Subtypes Through the Analysis of Multi-Omics Data with Adversarial Autoencoders. - Xia Chen; Hao Nie; Quanwei Chen; Xiang Zhang; Zixing He; Xiuxiu Chao; Weihao Ou; Xiangzheng Fu; Haowen Chen (J. Comput. Biol., 2025)

MultiCTox: Empowering Accurate Cardiotoxicity Prediction through Adaptive Multimodal Learning. - Lin Feng; Xiangzheng Fu; Zhenya Du; Yuting Guo; Linlin Zhuo; Yan Yang; Dong-Sheng Cao 001; Xiaojun Yao (J. Chem. Inf. Model., 2025)

metaCDA: A Novel Framework for CircRNA-Driven Drug Discovery Utilizing Adaptive Aggregation and Meta-Knowledge Learning. - Li Peng; Huaping Li; Sisi Yuan; Tao Meng; Yifan Chen; Xiangzheng Fu; Dongsheng Cao 001 (J. Chem. Inf. Model., 2025)

GH-UNet: group-wise hybrid convolution-VIT for robust medical image segmentation. - Shengxiang Wang; Ge Li; Min Gao; Linlin Zhuo; Mingzhe Liu 001; Zhizhong Ma; Wei Zhao; Xiangzheng Fu (npj Digit. Medicine, 2025)

AEGNN-M:A 3D Graph-Spatial Co-Representation Model for Molecular Property Prediction. - Lijun Cai; Yuling He; Xiangzheng Fu; Linlin Zhuo; Quan Zou 001; Xiaojun Yao (IEEE J. Biomed. Health Informatics, 2025)

CardiOT: Towards Interpretable Drug Cardiotoxicity Prediction Using Optimal Transport and Kolmogorov-Arnold Networks. - Xinyu Zhang; Hao Wang; Zhenya Du; Linlin Zhuo; Xiangzheng Fu; Dongsheng Cao 001; Boqia Xie; Keqin Li 001 (IEEE J. Biomed. Health Informatics, 2025)