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. DOI: https://doi.org/10.1093/bib/bbaf669.

2. Hongfei Li , Lingyu Cui, Murong Zhou, Quan Zou, Yuming Zhao, Hao Lin, Yingjian Liang, Chieh Kow Alfred Wei, Guohua Wang*. 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