2025：

1. 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. (中科院大类一区，影响因子14.1，TOP期刊)

2. Yunyun Su, Xiuhao Fu, Leyi Wei, Zilong Zhang*, Quan Zou*, Feifei Cui*. PROTCROWN: A Manually Curated Resource of Protein Corona Data for Unlocking the Potential of Protein–Nanoparticle Interactions. Nano Letters 2025; 25(5):1739-1744 (自然指数期刊，影响因子14.1，TOP期刊)

3. Chao Yang, Xiuhao Fu, Zhenjie Luo, Leyi Wei, Jingbing Li, Feifei Cui, Quan Zou, Qingchen Zhang, Zilong Zhang*. GCNLA: Inferring Cell-Cell Interactions From Spatial Transcriptomics With Long Short-Term Memory and Graph Convolutional Networks. IEEE Journal of Biomedical and Health Informatics 2025:1-14. (中科院小类一区，影响因子6.8，TOP期刊)

4. Yuanhao Li, Aoyun Geng, Zheyu Zhou, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Qingcheng 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. (TOP期刊，影响因子5.3)

5. Shun Gao, Yan Xia, Xingfeng Li, Feifei Cui, Qingchen Zhang, Quan Zou, Zilong Zhang*. ACP-ESM2: Enhancing Anticancer Peptide Prediction with Pre-trained Protein Language Models. IEEE Transactions on Computational Biology and Bioinformatics 2025:1-14. (CCF-B期刊)

6. Chunyan Cui, Feifei Cui, Quan Zou, Zilong Zhang*, Linpei Jia*. Progress and applications of single-cell RNA sequencing and spatial transcriptome technology in acute kidney injury research. Molecular Therapy Nucleic Acids 2025; 36(3) (TOP期刊，影响因子6.4)

7. Yan Xia, An Xiong, Zilong Zhang*, Quan Zou*, Feifei Cui*. A comprehensive review of deep learning-based approaches for drug–drug interaction prediction. Briefings in Functional Genomics 2025; 24:elae052

8. Shun Gao, Yanna Jia, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Qingchen Zhang, Quan Zou, Zilong Zhang*. PLPTP: A Motif-based Interpretable Deep Learning Framework Based on Protein Language Models for Peptide Toxicity Prediction. Journal of Molecular Biology 2025; 437(12):169115

9. Jian Liu, Aoyun Geng, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Qingchen Zhang, Quan Zou, Zilong Zhang*. NeuroCL: A deep learning approach for identifying neuropeptides based on contrastive learning. Analytical Biochemistry 2025; 705:115920

2024：

1. Xiuhao Fu, Chao Yang, Yunyun Su, Chunling Liu, Haoye Qiu, Yanyan Yu, Gaoxing Su, Qingchen Zhang, Feifei Cui*, Quan Zou*, Zilong Zhang*. Machine Learning Enables Comprehensive Prediction of the Relative Protein Abundance of Multiple Proteins on the Protein Corona. Research; 7:0487.(中科院大类一区，影响因子10.7，TOP期刊)

2. Yazi Li, Xiaoman Wei, Qinglin Yang, An Xiong, Xingfeng Li, Quan Zou, Feifei Cui*, Zilong Zhang*. msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths. BMC Biology 2024; 22(1):126. (中科院大类一区，影响因子5.4，TOP期刊)

3. Cuilin Xiao, Zheyu Zhou, Jiayi She, Jinfen Yin, Feifei Cui, Zilong Zhang*. PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset. International Journal of Biological Macromolecules 2024; 277:134317. (中科院大类一区，影响因子7.7, TOP期刊)

4. Zheyu Zhou, Cuilin Xiao, Jinfen Yin, Jiayi She, Hao Duan, Chunling Liu, Xiuhao Fu, Feifei Cui, Qi Qi, Zilong Zhang*. PSAC-6mA: 6mA site identifier using self-attention capsule network based on sequence-positioning. Computers in Biology and Medicine, 2024, 171:108129. (中科院小类一区，影响因子7.7，TOP期刊)

5. Hao Duan, Qingchen Zhang, Feifei Cui*, Quan Zou*, Zilong Zhang*. MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. PLOS Computational Biology 2024; 20(9):e1012409. (CCF-B推荐期刊)

6. Xiuhao Fu, Hao Duan, Xiaofeng Zang, Chunling Liu, Xingfeng Li, Qingchen Zhang, Zilong Zhang*, Quan Zou*, Feifei Cui*. Hyb_SEnc: An Antituberculosis Peptide Predictor Based on a Hybrid Feature Vector and Stacked Ensemble Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2024:1-17. (CCF-B期刊)

7. Chaorui Yan, Yanxu Zhu, Miao Chen, Kainan Yang, Feifei Cui*, Quan Zou*, Zilong Zhang*. Integration Tool for scRNA-seq Data and Spatial Transcriptomics Sequencing Data. Briefings in Functional Genomics, 2024:elae002. (影响因子4.0)

8. Xiuhao Fu, Ye Yuan, Haoye Qiu, Haodong Suo, Yingying Song, Anqi Li, Yupeng Zhang, Cuilin Xiao, Yazi Li, Lijun Dou, Zilong Zhang*, Feifei Cui*. AFG-PPIS: A Protein-protein Interaction Site Predictor Based on Attention Mechanism and Graph Convolutional Networks. Methods, 2024, YMETH 5447. (影响因子4.8)

9. Hao duan, Xiuhao Fu, Chunling Liu, Xiaofeng Zang, Anqi Xu, Xingfeng Li, Qingchen Zhang, Zilong Zhang*, Feifei Cui*. Machine learning-based prediction model for distant metastasis of breast cancer. Computers in Biology and Medicine, 169, 107943 (2024). (中科院小类一区，影响因子7.7，TOP期刊)

10. Yidi Sun, Lingling Kong, Jiayi Huang, Hongyan Deng, Xinling Bian, Xingfeng Li, Feifei Cui, Lijun Dou, Chen Cao, Quan Zou*, Zilong Zhang*. A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data. Briefings in Functional Genomics 2024:elae023.

11. Yidi Sun, Zhuoyu Pan, Ziyi Wang, Haofei Wang, Leyi Wei, Feifei Cui*, Quan Zou*, Zilong Zhang*. Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes. Journal of Translational Medicine 2024, 22(1):894.(影响因子7.5，Top期刊)

12. Ziyi Wang, Aoyun Geng, Hao Duan, Feifei Cui, Quan Zou, Zilong Zhang*. A Comprehensive Review of Approaches for Spatial Domain Recognition of Spatial Transcriptomes. Briefings in Functional Genomics 2024, 23(6):702-712. (影响因子4.0)

2023：

1. Yunyun Su, Shiyu Yan, Chen Cao, Feifei Cui, Quan Zou*, Zilong Zhang*. Human-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 5-8 Dec. 2023 2023. 293-298. (CCF-B推荐会议)

2. Ruiqi Liu, Xiuhao Fu, Shankai Yan, Zilong Zhang, Feifei Cui*. AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies. (Under review)

Before 2022：

1. Zilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, Quan Zou*. webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. Bioinformatics. 2022, Doi: 10.1093/bioinformatics/btac350.（生物信息学顶刊，IF=6.937）

2. Zilong Zhang, Feifei Cui, Chunyu Wang, Lingling Zhao*, Quan Zou*. Goals and approaches for each processing step for single-cell RNA sequencing data. Briefings in Bioinformatics. 2021, 22(4): bbaa314. (中科院一区，IF=13.994，TOP期刊)

3. Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, Quan Zou*. Critical downstream analysis steps for single-cell RNA sequencing data. Briefings in Bioinformatics. 2021, 22(5): bbab105. (中科院一区，IF=13.994，TOP期刊)

4. Zilong Zhang, Feifei Cui, Song Wu*, Quan Zou*. Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. Computers in Biology and Medicine. 2021, 140: 105092. (IF=4.589)

5. Zilong Zhang, Feifei Cui, Murong Zhou, Song Wu*, Quan Zou*, Bo Gao*. Single-cell RNA sequencing analysis identifies key genes in brain metastasis from lung adenocarcinoma. Current Gene Therapy. 2021, 21(4): 338-48.（IF=4.391）

6. Lijun Dou, Zilong Zhang, Lei Xu, Quan Zou. iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss. Computational and Structural Biotechnology Journal. 2022, 20:3268-3279. (IF=7.271)

7. Feifei Cui, Zilong Zhang, Quan Zou*. Sequence representation approaches for sequence-based protein prediction tasks that use deep learning. Briefings in Functional Genomics. 2021, 20(1): 61-73. (IF=4.241)

8. Feifei Cui, Zilong Zhang, Chen Cao, Quan Zou, Dong Chen*, Xi Su*. Protein-DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data. Proteomics. 2022, 3: e2100197. Doi: 10.1002/pmic.202100197. (IF=4.044)

9. Chen Cao, Jianhau Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou*. webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. Nucleic acids research. 2022, 50(D1): D1123-D1130. (中科院分区一区，IF=16.971，TOP期刊)

10. Kunsen Lin, Youcai Zhao, Jia-Hong Kuo, Hao Deng, Feifei Cui, Zilong Zhang, Meilan Zhang, Chunlong Zhao, Xiaofeng Gao*, Tao Zhou*, Tao Wang*. Toward smarter management and recovery of municipal solid waste: A critical review on deep learning approaches. Journal of Cleaner Production, 2022: p. 130943. (中科院分区一区, IF=9.297)

11. Feifei Cui, Shuang Li, Zilong Zhang, Miaomiao Sui, Chen Cao, Abd El-Latif Hesham, Quan Zou, DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins. Computational and Structural Biotechnology Journal. 2022, 20: 2020-2028. (IF=7.271)

12. Wei Sun, Zilong Zhang, Xin liu, Shuang Zhang, Lu He, Zhe Wang, Guangshu Wang*. Terpene glycosides from the roots of Sanguisorba officinalis L. and their hemostatic activities. Molecules (Basel, Switzerland). 2012, 17(7): 7629-36. (IF=4.411)

13. Zheng Chen, Zijie Shen, Zilong Zhang, Da Zhao, Lei Xu* and Lijun Zhang*. RNA-associated co-expression network identifies novel biomarkers for digestive system cancer. Frontiers in Genetics. 2021, 12: 659788（IF=4.599）