2024年度

1. Yazi Li, Xiaoman Wei, Qinglin Yang, An Xiong, Xingfeng Li, Quan Zou, Feifei Cui*, and 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): p. 126. (中科院大类一区，影响因子5.4，TOP期刊)

2. Hao Duan, Qingchen Zhang, Feifei Cui*, Quan Zou*, and Zilong Zhang*. MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. PLOS Computational Biology, 2024. 20(9): p. e1012409. （生物信息学经典期刊，影响因子3.97）

3. Xiuhao Fu, Chao Yang, Yunyun Su, Chunling Liu, Haoye Qiu, Yanyan Yu, Gaoxing Su, Qingchen Zhang, Leyi Wei, and Feifei Cui*, Quan Zou* and Zilong Zhang*. Machine learning enables comprehensive prediction of the relative protein abundance of multiple proteins on the protein corona. Research, 2024. (中科院大类一区，影响因子8.5)

4. Chaorui Yan, Aoyun Geng, Zhuoyu Pan, Zilong Zhang, and Feifei Cui*. MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides. Briefings in Bioinformatics, 2024. 25(6): p. bbae505. (中科院小类一区，影响因子6.8，TOP期刊)

5. Jiahao Yuan, Ziyi Wang, Zhuoyu Pan, Aohan Li, Zilong Zhang, and Feifei Cui*. DPNN-ac4C: A Dual-Path Neural Network with self-attention mechanism for identification of N4‑acetylcytidine (ac4C) in mRNA. Bioinformatics, 2024: p. btae625. (生物信息学顶刊，影响因子4.4)

6. Xiuhao Fu, Xiaofeng Zang, Chunling Liu, Xingfeng Li, Qingchen Zhang, Zilong Zhang*, Quan Zou*, and 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. (CCF-B期刊，影响因子3.6)

7. Xiuhao Fu, Ye Yuan, Haoye Qiu, Haodong Suo, Yingying Song, Anqi Li, Yupeng Zhang, Cuilin Xiao, Yazi Li, Lijun Dou, Zilong Zhang* and Feifei Cui*. AGF-PPIS: a protein–protein interaction site predictor based on an attention mechanism and graph convolutional networks. Methods, 2024. 222: p. 142-151. (影响因子4.2)

8. Hao Duan, Yu Zhang, Haoye Qiu, Xiuhao Fu, Chunling Liu, Xiaofeng Zang, Anqi Xu, Ziyue Wu, Xingfeng Li, Qingchen Zhang, Zilong Zhang and Feifei Cui*. Machine learning-based prediction model for distant metastasis of breast cancer. Computers in Biology and Medicine. 2024. 169: 107943. (中科院小类一区，影响因子7.0，TOP期刊)

9. Yidi Sun, Zhuoyu Pan, Ziyi Wang, Haofei Wang, Leyi Wei, Feifei Cui*, Quan Zou*, and 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): p. 894. (影响因子6.1，TOP期刊)

10. Chaorui Yan, Yanxu Zhu, Miao Chen, Kainan Yang, Feifei Cui*, Quan Zou*, and Zilong Zhang*. Integration tools for scRNA-seq data and spatial transcriptomics sequencing data. Briefings in Functional Genomics, 2024. 23(4): p. 295-302. (影响因子4.0)

11. Cuilin Xiao, Zheyu Zhou, Jiayi She, Jinfen Yin, Feifei Cui, and 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: p. 134317. (中科院大类一区，影响因子7.7, TOP期刊)

12. Zheyu Zhou, Cuilin Xiao, Jinfen Yin, Jiayi She, Hao Duan, Chunling Liu, Xiuhao Fu, Feifei Cui, Qi Qi, and 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7.0，TOP期刊)

13. Yidi Sun, Lingling Kong, Jiayi Huang, Hongyan Deng, Xinling Bian, Xingfeng Li, Feifei Cui, Lijun Dou, Chen Cao, Quan Zou and Zilong Zhang*. A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data. Briefings in Functional Genomics, 2024: p. elae023. (影响因子4.0)

14. Chen Cao, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, and Rui Fan. RAVAR: a curated repository for rare variant–trait associations. Nucleic Acids Research, 2024. 52(D1): p. D990-D997. (影响因子16.6，TOP期刊)

2023年度及以前

15. Ruiqi Liu, Xiuhao Fu, Shankai Yan, Zilong Zhang, and Feifei Cui*. AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies. in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Istanbul, Turkiye, 2023, pp. 23-29.

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

17. Zhibin Lv^#, Feifei Cui^#, Quan Zou*, Lichao Zhang*, Lei Xu*. Anticancer peptides prediction with deep representation learning features. Briefings in Bioinformatics. 2021, 22(5): 1-14. (IF=13.994，中科院一区Top 期刊)

18. 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，中科院二区)

19. 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)

20. 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=3.984)

21. Feifei Cui, Liang Cheng*, Quan Zou*. Briefings in functional genomics special section editorial: analysis of integrated multiple omics data. Briefings in Functional Genomics. 2021, 20(4): p. 196-197. (IF=4.241)

22. Feifei Cui, Quan Zou*. Biocomputing and Synthetic Biology in Cells: Cells Special Issue. Cells. 2020, 9(11): 2459. (IF=4.326)

23. Feifei Cui, Quan Zou*, Qin Ma, Leyi Wei, Jijun Tang and Dariusz Mrozek. IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis. IEEE Access. 2021, 9: 33110-33119. (IF=3.367)

24. Feifei Cui, Murong Zhou, Quan Zou*. Computational biology and chemistry Special section editorial: Computational analyses for miRNA. Computational Biology and Chemistry. 2021, 91:107448. (IF=2.877)

25. Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, and Quan Zou. Critical downstream analysis steps for single-cell RNA sequencing data. Briefings in Bioinformatics, 2021. 22(5): p. bbab105.

26. Zilong Zhang, Feifei Cui, Chunyu Wang, Lingling Zhao, and Quan Zou. Goals and approaches for each processing step for single-cell RNA sequencing data. Briefings in Bioinformatics, 2021. 22(4): p. bbaa314.

27. Zilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, and Quan Zou. webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. Bioinformatics, 2022. 38(13): p. 3488-3489.

28. Zilong Zhang, Feifei Cui, Murong Zhou, Song Wu, Quan Zou, and Bo Gao. Single-cell RNA Sequencing Analysis Identifies Key Genes in Brain Metastasis from Lung Adenocarcinoma. Current Gene Therapy, 2021. 21(4): 338-348.

29. Zilong Zhang, Feifei Cui, Chen Cao, Qingsuo Wang, and 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, 2022. 140: 105092.

30. Chen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, and Quan Zou. webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. Nucleic Acids Research, 2021: p. gkab957.

31. Kunsen Lin, Youcai Zhao, Jia-Hong Kuo, Hao Deng, Feifei Cui, Zilong Zhang, Meilan Zhang, Chunlong Zhao, Xiaofeng Gao, and Tao Zhou. Toward smarter management and recovery of municipal solid waste: A critical review on deep learning approaches. Journal of Cleaner Production, 2022. 346: p. 130943.

32. Kunsen Lin, Youcai Zhao, Lina Wang, Wenjie Shi, Feifei Cui, and Tao Zhou. MSWNet: A visual deep machine learning method adopting transfer learning based upon ResNet 50 for municipal solid waste sorting. Frontiers of Environmental Science & Engineering, 2023. 17(6): p. 77.