Leyi Wei, Pengwei Xing, Ran Su, Gaotao Shi, Zhanshan (Sam) Ma*, Quan Zou*. CPPred-RF: a sequence-based predictor for identifying cell-penetrating peptides and their uptake efficiency. Journal of Proteome Research.2017, 16(5):2044-2053.
Leyi Wei, Jijun Tang, Quan Zou*. SkipCPP-Pred: An Improved and Promising Sequence-based Predictor for Predicting Cell-Penetrating Peptides. BMC Genomics. 2017, 18 (Suppl 7): 742
Leyi Wei, Jie Hu, Fuyi Li, Jiangning Song*, Ran Su*, Quan Zou*. Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. Briefings in Bioinformatics. 2020,21(1): 106-119
Ran Su, Jie Hu, Quan Zou, Balachandran Manavalan, Leyi Wei. Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools. Briefings in Bioinformatics. 2020, 21(2): 408-420
Leyi Wei*, Chen Zhou, Ran Su*, Quan Zou*. PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning. Bioinformatics. 2019, 35(21):4272-4280
Chunyan Ao, Yu Zhang, Dapeng Li, Yuming Zhao*, Quan Zou*. Progress in the development of antimicrobial peptide prediction tools. Current protein & peptide science. 2021, 22(3): 211-216
Xiangzheng Fu, Lijun Cai, Xiangxiang Zeng*, Quan Zou*. StackCPPred: A Stacking and Pairwise Energy Content based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency. Bioinformatics.2020, 36(10): 3028-3034
Changli Feng, Quan Zou*, Donghua Wang*. Using a Low Correlation High Orthogonality Feature Set and Machine Learning Methods to Identify Plant Pentatricopeptide Repeat Coding Gene/Protein. Neurocomputing. 2021, 424: 246-254
Jiawei Li, Yuqian Pu, Jijun Tang, Quan Zou*, Fei Guo*. DeepAVP: a dual-channel deep neural network for identifying variable-length antiviral peptides. IEEE Journal of Biomedical and Health Informatics. 2020, 24(10): 3012-3019
Yu Zhang, Quan Zou*. PPTPP: A novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning. Bioinformatics. 2020, 36(13): 3982-3987
Lijun Cai, Li Wang, Xiangzheng Fu*, Chenxing Xia, Xiangxiang Zeng, Quan Zou. ITP-Pred: An interpretable method for predicting therapeutic peptides with fused features low-dimension represention. Briefings in Bioinformatics. 2021, 22(4): bbaa367
Zhibin Lv, Feifei Cui, Quan Zou*, Lichao Zhang*, Lei Xu*. Anti-Cancer Peptide Prediction with Deep Representation Learning Features. Briefings in Bioinformatics. 2021, 22(5): bbab008.
Xiaoyi Guo, Yizhang Jiang*, Quan Zou*. Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides. Briefings in Bioinformatics. 2022, 23(3): bbac135
Hongwu Lv, Ke Yan, Yichen Guo, Quan Zou, Abd EI-Latif Hesham, Bin Liu. AMPpred-EL: An effective antimicrobial peptide prediction model based on ensemble learning. Computers in Biology and Medicine. 2022, 146: 105577
Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai*, Leyi Wei*. Predicting protein-peptide binding residues via interpretable deep learning. Bioinformatics. 2022, 38(13):3351-3360
Peng Liu, Shulin Zhao, Quan Zou, Yijie Ding*. Prediction of Cell-Penetrating Peptides Using a Novel HSIC-Based Multiview TSK Fuzzy System. Applied Sciences. 2022, 12(11):5383.
Xiaoyi Guo, Prayag Tiwari*, Quan Zou*, Yijie Ding*. Subspace projection-based weighted echo state networks for predicting therapeutic peptides. Knowledge Based Systems. 2023, 263:110307
Yi Jiang, Ruheng Wang, Jiuxin Feng, Junru Jin, Sirui Liang, Zhongshen Li, Yingying Yu, Anjun Ma, Ran Su, Quan Zou, Qin Ma*, Leyi Wei*. Explainable Deep Hypergraph Learning Modeling the Peptide Secondary Structure Prediction. Advanced Science. 2023, 2206151.
Jici Jiang, Jiayu Li, Junxian Li, Hongdi Pei, Mingxin Li, Quan Zou*, Zhibin Lv *. A robust machine learning method to identify umami peptides accurately with sequences embedded by multiplicative LSTM. Foods. 2023, 12(7): 1498
Zhongsheng Li, Junru Jin, Wenjia He, Wentao Long, Haoqing Yu, Xin Gao, Kenta Nakai, Quan Zou*, Leyi Wei*. CoraL: Interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Briefings in Bioinformatics. 2023, 24(6): bbad352
Changjiang Li, Quan Zou, Cangzhi Jia*, Jia Zheng*. AMPpred-MFA: An Interpretable Antimicrobial Peptide Predictor with a Stacking Architecture, Multiple Features, and Multihead Attention. Journal of Chemical Information and Modeling. 2024, 64(7): 2393-2404
Ali Raza, Jamal Uddin, Abdullah Almuhaimeed, Shahid Akbar*, Quan Zou*, Ashfaq Ahmad. AIPs-SnTCN: Predicting Anti-inflammatory Peptides Using Fast Text and Transformer Encoder-based Hybrid Word Embedding with Self-normalized Temporal Convolutional Networks. Journal of Chemical Information and Modeling. Doi: 10.1021/acs.jcim.3c01563
Jici Jiang, Hongdi Pei, Jiayu Li, Mingxin Li, Quan Zou*, Zhibin Lv*. FEOpti-ACVP: Identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization. Briefings in Bioinformatics. 2024,25(2): bbae037
Ali Raza, Jamal Uddin, Shahid Akbar*, Fawaz Khaled Alarfaj, Quan Zou*, Ashfaq Ahmad. Comprehensive Analysis of Computational Methods for Predicting Anti-inflammatory Peptides. Archives of Computational Methods in Engineering. 2024, 31: 3211-3229
Shahid Akbar, Ali Raza, Quan Zou*. Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking mode. BMC Bioinformatics. 2024, 25: 102
Shahid Akbar, Quan Zou*, Ali Raza, Fawaz Khaled Alarfaj. iAFPs-Mv-BiTCN: Predicting antifungal peptides using self-attention transformer embedding and transform evolutionary based multi-view features with bidirectional temporal convolutional networks. Artificial Intelligence in Medicine. 2024, 151: 102860
Rui Wang, Tao Wang, Linlin Zhuo*, Jinhang Wei, Xiangzheng Fu*, Quan Zou*, Xiaojun Yao*. Diff-AMP: Tailored Designed Antimicrobial Peptide Framework with All-in-One Generation, Identification, Prediction and Optimization. Briefings in Bioinformatics. 2024, 25(2): bbae078
Xiaoyi Guo, Ziyu Zheng, Kang Hao Cheong, Quan Zou, Prayag Tiwari*, Yijie Ding*. Sequence homology score-based deep fuzzy network for identifying therapeutic peptides. Neural Networks. 2024, 178: 106458
Li Wang, Yiping Liu*, Xiangzheng Fu*, Xiucai Ye, Junfeng Shi, Gary G Yen, Quan Zou, Xiangxiang Zeng, Dongsheng Cao. HMAMP: Designing Highly Potent Antimicrobial Peptides Using a Hypervolume-Driven Multiobjective Deep Generative Model. Journal of Medicinal Chemistry. 2025, 68(8): 8346-8360
Zhenjie Luo, Aoyun Geng, Leyi Wei, Quan Zou, Feifei Cui*, Zilong Zhang*. CPL-Diff: A Diffusion Model for De Novo Design of Functional Peptide Sequences with Fixed Length. Advanced Science. 2025, 12(20): 2412926
Yuanhao Li, Aoyun Geng, Zheyu Zhou, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Qingchen Zhang, Zilong Zhang*. AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. Journal of Chemical Information and Modeling. 2025, 65(12): 5868-5886
Haotian Wang, Rujun Li, Qiunan Yu, Liangzhen Jiang, Ximei Luo, Quan Zou, Zhibin Lv*. iAVP-RFVOT: Identify Antiviral Peptides by Random Forest Voting Machine Learning with Unified Manifold Learning Embedded Features. Biochemistry. 2025, 64(14): 3137-3147
Shihu Jiao, Xiucai Ye*, Tetsuya Sakurai, Quan Zou, Wu Han*, Chao Zhan*. Integration of pre-trained protein language models with equivariant graph neural networks for peptide toxicity prediction. BMC Biology. 2025, 23: 229
Qianmao Wen, Aoyun Geng, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Feifei Cui*. DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms. Journal of Chemical Information and Modeling. 2025, 65(19): 10011-10024
Shahid Akbar, Ali Raza, Quan Zou, Wajdi Alghamdi, Xiaorui Kang, Hashim Ali, Ximei Luo*. Accelerating prediction of antiviral peptides using genetic algorithm-based weighted multi-perspective descriptors with Self-normalized Deep Networks. Journal of Chemical Information and Modeling. 2005, 65(18): 9815-9830
Yongqing Zhang, Xinyu Mao,Yuhang Liu, Wang Li, Zhigan Zhou, Yugui Xu, Jin Wu, Quan Zou, Lei Xu*. Explainable multiscale representation learningfor anticancer peptide prediction. Engineering Applications of Artificial Intelligence. 2026, 167(2): 113827
Qianmao Wen, Xinyu Li, Jiaxiang Song, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Feifei Cui*. Computational methods for signal peptide prediction: From statistical models to deep learning. Biotechnology Advances. 2026, 88: 108819
Shahid Akbar, Ali Raza, Matee Ullah, Wajdi Alghamdi, Mukhtaj Khan, Quan Zou*. Deep capsule neural network for identifying anticancer peptides using sequence to image transformation-based local embedded features. BMC Biology. 2026, 24: 70
Binyu Li, Xin Zhang, Zhihua Huang, Prayag Tiwari, Quan Zou, Yijie Ding*, Xiaoyi Guo*. Enhancing Anticancer Peptide Discovery: A Fusion-Centric Framework with Conditional Diffusion for Prediction and Generation. PLoS Computational Biology. 2026, 22(3): e1014098
Wenyu Zhang, Yizheng Wang, Yixiao Zhai, Pinglu Zhang, Yijie Ding*, Quan Zou*. A Unified Framework for Potency-Oriented AMP Discovery via Multi-Modal Learning and Guided Sequence Synthesis. PLoS Computational Biology. 2026, 22 (9): e1014771