Ph.D., Bioinformatics, “The process, analysis and integration of transcriptome and proteome data”, Fudan University (FDU), Shanghai, China, 2010.
Master of Engineering, Biochemical Engineering, “Synthesis of hepatic targeting antineoplastic agent galactosylated-taxol”, Huazhong University of Science and Technology (HUST), Wuhan, China, 2003.
Bachelor of Science, Biochemistry, South-Central University for Nationalities, Wuhan, China, 2000.
Appointments
2022.11～present, Associate Researcher, Intelligent Medicine Institute, FDU, China.
2020.1～present,Member of a Committee, Special Committee on Hereditary Gastrointestinal Neoplasms, Shanghai Anti-Cancer Association, Shanghai, China.
2018.1～2022.12, Primary Investigator, Centre Laboratory, Affiliated Hospital of Dermatology, Tongji University, Shanghai, China.
2017.1～2018.12, Primary Investigator, Department of Gastroenterology, Songjiang Hospital Affiliated First People's Hospital, Shanghai Jiao Tong University, Shanghai, China.
2016.1～2021.12, Member of a Council, Chinese Human Proteome Organization (CNHUPO), China.
2014.9～2016.8, Postdoctoral Researcher, Department of Biosciences and Nutrition, Karolinska Institutet, Sweden.
2014.5～present, Associate Researcher, Department of Systems Biology for Medicine, Shanghai Medical College, FDU, China.
2012.12～2022.10, Associate Researcher, Institutes of Biomedical Science, FDU, China.
2012.11～2019.12, Academician, Bioinformatics Council of CNHUPO, China.
2008.7～2012.11, Assistant Researcher, Institutes of Biomedical Science, FDU, China.
2005.3～2008.6, PhD Candidate, Department of Chemistry, FDU, China.
2003.8～2005.3, Lab Technician, State Key Laboratory of Proteomics, Beijing Proteome Research Centre, China.
2002.3～2003.5, Visiting Graduate Student, Beijing Institute of Pharmacology and Toxicology, China.
2000.9～2003.6, Graduate Student, School of Life Science and Technology, HUST, China.
1996.9～2000.6, Undergraduate Student, Department of Chemistry, South-Central University for Nationalities, China.
Achievements
Zhong presided over one National Natural Science Foundation of China (NSFC) and one “Shanghai Health Bureau Project”, and participated in one sub-project each of the 11th and 12th Five-Year Plan of the National Major Special Project on Infectious Diseases, as well as two “National Key Research and Development Program of China”, three “973”, one “863”, one “Program of International S&T Cooperation”, one military-industrial project, one integration project of the “Major Research Plan of the NSFC”, and one project of the “Shanghai Science and Technology Innovation Action Plan”. The total amount of scientific research funding is 12.68 million RMB. Zhong have published 28 SCI papers as responsible authors and other 29 SCI papers as signed authors, with total citations of ~3,000 and H-index of 24. Zhong have obtained 2 domestic invention patents and 1 software copyright, and applied for 4 domestic invention patents. He has introduced and participated in the translation of two academic monographs. He has been invited as a reviewer by Journal of Cellular Physiology, BMC Biology, BMC Genomic Data, Scientific Reports, Therapeutic Medicine and other academic journals.
Research Directions
1. Biomedical knowledge graph inference based on deep learning methods.
2. Drug repositioning and new drug development based on knowledge graph inference.
3. Development of disease prediction and diagnosis models based on multimodal data fusion.
4. Development of biomedical foundational model and explainable artificial intelligence.
5. Knowledge discovery based on multi-omics data and biomolecular networks.
Publications in 5 years
1. Huang Y, Zhong F*, Liu L. Uncovering latent biological function associations through gene set embeddings. BMC Bioinformatics. 2025 Mar 24;26(1):90.
2. Li Y, Xiong J, Hu Z, Chang Q, Ren N*, Zhong F*, Dong Q*, Liu L*. Denoised recurrence label-based deep learning for prediction of postoperative recurrence risk and sorafenib response in HCC. BMC Med. 2025 Mar 18;23(1):162.
3. Xia X, Zhu C, Zhong F*, Liu L*. TransCDR: a deep learning model for enhancing the generalizability of drug activity prediction through transfer learning and multimodal data fusion. BMC Biol. 2024;22(1):227-247.
4. Zhang Y, Zhong F*, Liu L*. Single-cell transcriptional atlas of tumor-associated macrophages in breast cancer. Breast Cancer Res. 2024;26:129.
5. Du D, Zhong F*, Liu L*. Enhancing recognition and interpretation of functional phenotypic sequences through fine-tuning pre-trained genomic models. J Transl Med. 2024;22(1):756.
6. Fu Q, Dong C, Liu Y, Xia X, Liu G, Zhong F*, Liu L*. A comparison of scRNA-seq annotation methods based on experimentally labeled immune cell subtype dataset. Brief Bioinform. 2024;25(5):bbae392.
7. Du D, Zhang Y, Zhong F*, Liu L*. Advances in Human Genome Resolution: The Role of Pan-Genomic Strategies and Fine-Tuning Pre-trained Genomic Models. Med Res Arch. 2024;12(7).
8. Zhu C, Xia X, Li N, Zhong F*, Yang Z*, Liu L*. RDKG-115: Assisting Drug Repurposing and Discovery for Rare Diseases by Trimodal Knowledge Graph Embedding. Comput Biol Med. 2023 Jul 17;164:107262.
9. Xia X, Zhu C, Zhong F*, Liu L*. MDTips: A Multimodal-data based Drug-Target interaction prediction system fusing knowledge, gene expression profile and structural data. Bioinformatics. 2023 Jul 1;39(7):btad411.
10. Zhu C, Yang Z, Xia X, Li N, Zhong F*, Liu L*. Multimodal reasoning based on knowledge graph embedding for specific diseases. Bioinformatics. 2022 Feb 12;38(8):2235-2245.
11. Sun C#, Mi Y#, Ge S#, Hu Q, Xu K, Guo Y, Tan Y, Zhang Y*, Zhong F*, Xia G*. Tumor- and Osteoblast-derived Periostin in Prostate Cancer Bone Metastases. Front Oncol. 2022 Jan 11;11: 795712.
12. Gong T#, Yang L#, Shen F#, Chen H, Pan Z, Zhang Q, Jiang Y, Zhong F*, Yang P*, Zhang Y*. Computational and Mass Spectrometry-Based Approach Identify Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in JMJD6. Molecules. 2021 July 31;26(15). 10.3390.
13. Tan Y#, Wang M#, Zhang Y, Ge S,Zhong F*, Xia G*, Sun C*. Tumor-associated macrophages: A potential target for cancer therapy. Front Oncol. 2021 Jun 10;11: 693517.
Participation in Research Projects in 5 years
1. Project under the Shanghai Science and Technology Innovation Action Plan in Computational Biology: “Construction of knowledge reasoning-enhanced multimodal medical large model and collaborative consultation application for major diseases”, (24JS2840200), Project Backbone, 2024.12-2027.11.
2. The National Key Research and Development Program of China topic “Development of clinical decision support system for precision medicine”, sub-topic “Development of generic technologies and platforms of clinical decision support system for precision medicine”, (2018YFC0910701), Project Backbone, 2018.7-2021.6.
3. The National Key Research and Development Program of China topic “Construction of a precision medicine knowledge base for disease research”, sub-topic “Construction of a precision medicine knowledge graph based on bioinformatics”, (2016YFC0901903),Project Backbone, 2016.1-2021.6.
Patents and Software
●Fan Zhong, Yang Liu, Ping Xu, Jing Wang, Yuexin Lai, Zhiwen Yang. A set of internal reference genes for relative quantification by real-time quantitative PCR applied to hepatocellular carcinoma and its screening method. Patent No. 201710971976.7. Chinese invention patent, 2021.02.19.
●Fan Zhong, Hailin Tang. PathPPI database platform v1.0. Software registration No. 2018SR241450. Software copyright, 2018.04.10.
●Fuchu He, Kaixuan Luo, Fan Zhong, Haijian Wang. A novel classification method of differential proteomics. Patent No. 200910052187.9. Chinese invention patent, 2013.02.27.
