Postdoc, Major in Computer Science and Technology Work Unit:Yangtze Delta Region Institute (Quzhou), UESTC, China Email: lihongfei@nefu.edu.cn Advisor: Professor Quan Zou

Education

• September 2020 - July 2024: PhD in Biology, NORTHEASTERN FORESTRY UNIVERSITY, China

• September 2017 - July 2020: Master in Software Engineering, HENAN NORMAL UNIVERSITY, China

• September 2013 - July 2017: Electronic Information Engineering, LESHAN NORMAL UNIVERSITY, China

Research

My research interests include

• bioinformation

• Single-cell multi-omics: scRNA, scATAC

• Deep Learning Technology

Publications

1. Hongfei Li, Jiechen Wang, Qin Liu, Quan Zou, Ximei Luo*. Assessment and Applications of Joint profiling of Single-Cell Chromatin Accessibility and Transcriptome. Briefings in Bioinformatics. 2025. (Under Review)

2. Li Hongfei, Cui Lingyu, Zhou Murong, Zou Quan, Zhao Yuming, Lin Hao, Liang Yingjian, Chieh Kow Alfred Wei, Wang Guohua*. Single-cell multi-omics data reveal heterogeneity in liver tissue microenvironment induced by hypertension. Molecular Therapy Nucleic Acids. 2025. DOI:https://doi.org/10.1016/j.omtn.2025.102696.

3. Hongfei Li, Zhang, Jingyu; Zhao, Yuming*; Yang, Wen*. Predicting Corynebacterium glutamicum Promoters Based on Novel Feature Descriptor and Feature Selection Technique. Frontiers in Microbiology. 2023. DOI:https://doi.org/10.3389/fmicb.2023.1141227.

4. Hongfei Li, Gong, Yue; Liu, Yifeng; Lin, Hao*; Wang, Guohua*. Detection of transcription factors binding to methylated DNA by deep recurrent neural network. Briefings in Bioinformatics. 2022. DOI:https://doi.org/10.1093/bib/bbab533.

5. Hongfei Li, Shi, Lei; Gao, Wentao; Zhang, Zixiao; Zhang, Lichao; Zhao, Yuming; Wang, Guohua*. dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost. Methods. 2022. DOI:https://doi.org/10.1016/j.ymeth.2022.01.001.

6. Hongfei Li, Wang, Xianfang; Tang, Hua*. Predicting Bacteriophage Enzymes and Hydrolases by Using Combined Features. Frontiers in Bioengineering and Biotechnology. 2020. DOI:https://doi.org/10.3389/fbioe.2020.00183.

7. Hongfei Li, Du, Haoze; Wang, Xianfang*; Gao, Peng; Liu, Yifeng; Lin, Weizhong. Remarks on Computational Method for Identifying Acid and Alkaline Enzymes. Current Pharmaceutical Design. 2020. DOI:https://doi.org/10.2174/1381612826666200427124519.

8. Jianmei Zhao#, Zeyu Zhao#, Hongfei Li#, Haojie Yu, Hao Lin, Hanqi Chen, Xuecang Li, Di Liu, Yiming Wang, Guohua Wang*. CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer. BMC Genomics. 2025. DOI:https://doi.org/10.1186/s12864-025-11849-7.

9. Jinyuan Li#, Hongfei Li#, Fang Wang, Lei Yuan, Yuming Zhao. scPPF: Predicting Promoter Fragments in scATAC-seq Based on Transcription Factor Motifs. Current Bioinformatics. 2025. DOI:10.2174/0115748936385361250710042542.

10. Ke, Jinsong#; Zhao, Jianmei#; Hongfei Li#; Yuan, Lei; Dong, Guanghui; Wang, Guohua*. Prediction of protein N-terminal acetylation modification sites based on CNN-BiLSTM-attention model. Computers in Biology and Medicine. 2024. DOI:https://doi.org/10.1016/j.compbiomed.2024.108330.

11. Zhang, Zixiao; Gong, Yue; Gao, Bo; Hongfei Li; Gao, Wentao; Zhao, Yuming; Dong, Benzhi*. SNAREs-SAP: SNARE Proteins Identification With PSSM Profiles. Frontiers in Genetics. 2021. DOI:https://doi.org/10.3389/fgene.2021.809001.

12. Zhang, Tianjiao; Jia, Yuran; Hongfei Li; Xu, Dali; Zhou, Jie; Wang, Guohua*. CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins. Briefings in Bioinformatics. 2022. DOI:https://doi.org/10.1093/bib/bbac335.

13. Zhu, Di; Yang, Wen; Xu, Dali; Hongfei Li; Zhao, Yuming*; Li, Dan*. A deep learning based two-layer predictor to identify enhancers and their strength. Methods. 2023. DOI:https://doi.org/10.1016/j.ymeth.2022.10.003.

14. Cui, Lingyu; Hongfei Li; Bian, Jilong; Wang, Guohua*; Liang, Yingjian*. Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer. Briefings in Bioinformatics. 2023. DOI:https://doi.org/10.1093/bib/bbad011.

15. Gao, Wentao; Xu, Dali; Hongfei Li; Du, Junping; Wang, Guohua*; Li, Dan*. Identification of adaptor proteins by incorporating deep learning and PSSM profiles. Methods. 2023. DOI:https://doi.org/10.1016/j.ymeth.2022.08.016.

16. Zhao, Hongxi; Hongfei Li; Liu, Qiaoming; Dong, Guanghui; Hou, Chang; Li, Yang*; Zhao, Yuming*. Using TransR to enhance drug repurposing knowledge graph for COVID-19 and its complications. Methods. 2024. DOI:https://doi.org/10.1016/j.ymeth.2023.09.007.

17. Zhou, Murong; Hongfei Li; Gao, Bo; Zhao, Yuming*. The prognostic impact of pathogenic stromal cell-associated genes in lung adenocarcinoma. Computers in Biology and Medicine. 2024. DOI:https://doi.org/10.1016/j.compbiomed.2024.108692.

18. Sun, Ailun; Hongfei Li; Dong, Guanghui; Zhao, Yuming*; Zhang, Dandan*. DBPboost: A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction. Methods. 2024. DOI:https://doi.org/10.1016/j.ymeth.2023.11.011.

19. Cui, Lingyu; Wang, Fang; Hongfei Li; Liu, Qiaoming; Zhou, Murong; Wang, Guohua*. annATAC: automatic cell type annotation for scATAC-seq data based on language model. BMC Biology. 2025. DOI:https://doi.org/10.1186/s12915-025-01866-y.

Awards

• National Scholarship for Graduate Students, 2019