代表性论文（>150篇 SCI 论文）：
1. Jinxin Liu, Mingyu Wang, Chentao Xu, Longhao Jia, Senying Lai, Zi-Chao Zhang, Jinglong Zhang, Wei-Hua Chen*, Yucheng T. Yang*, Xing-Ming Zhao*. HGMT: a database of human gut microbiota for tumors and immunotherapy response. Genome Biology. 2025, 26(1):401.
2. Zhengyu An, Tianhong Zhang, Xiaochen Tang, Lihua Xu, Jing Ding, Jijun Wang, Jie Zhang, Jingqi Chen*, Xing-Ming Zhao*. Characterizing schizophrenia-relevant structural variants and tandem repeats through long-read sequencing. Science Bulletin. 2025, S2095-9273(25)01110-7.
3. Xingzhong Zhao, Anyi Yang, Jing Ding*, Yucheng T. Yang*, Xing-Ming Zhao*. Regulatory Genomic Circuitry of Brain Age by Integrative Functional Genomic Analyses. Genomics Proteomics Bioinformatics. 2025, qzaf064.
4. Longhao Jia, Yize Ke, Shuo Zhao, Jinxin Liu, Xiaohui Luo, Jixin Cao, Yujia Liu, Qihao Guo, Wei-Hua Chen, Feng Chen, ZIB Consortium, Jiao Wang*, Hao Wu*, Jing Ding*, Xing-Ming Zhao*. Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease. Molecular Psychiatry, 2025, 30(9):3951-3962.
5. Jinglong Zhang, Jiao Wang, Qiongjie Zhou, Zixin Chen, Junyi Zhuang, Xingzhong Zhao, Ziquan Gan, Yinan Wang, Chunxiu Wang, Robert S. Molday, Yucheng T. Yang*, Xiaotian Li*, Xing-Ming Zhao*. Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development. Nature Communications, 2025, 16(1):2307.
6. Jixin Cao, Cheng Zhang, Chun-Yi Zac Lo, Qihao Guo, Jing Ding, Xiaohui Luo, Zi-Chao Zhang, Feng Chen, ZIB Consortium, Tian-Lin Cheng*, Jingqi Chen*, Xing-Ming Zhao*. Alzheimer's Disease Neuroimaging Initiative. Integrating rare pathogenic variant prioritization with gene-based association analysis to identify novel genes and relevant multimodal traits for Alzheimer's disease. Alzheimer's & Dementia,2025, 21(2):e14444.
7. Huarui Wang, Chuqing Sun, Yun Li, Jingchao Chen, Xing-Ming Zhao*, Wei-Hua Chen*. Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners. Microbiome, 2024, 12(1):260.
8. Yiqian Duan, Celio Dias Santos-Júnior, Thomas Sebastian Schmidt, Anthony Fullam, Breno L. S. de Almeida, Chengkai Zhu, Michael Kuhn, Xing-Ming Zhao*, Peer Bork*, Luis Pedro Coelho*. A catalog of small proteins from the global microbiome. Nature Communications, 2024, 15(1):7563.
9. Jingchao Chen, Chuqing Sun, Yanqi Dong, Menglu Jin, Senying Lai, Longhao Jia, Xueyang Zhao, Huarui Wang, Na L. Gao, Peer Bork, Zhi Liu*, Wei-Hua Chen*, Xing-Ming Zhao*.Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing. Advanced Science, 2024, 11(13): e2305818.
10. Jiaying Zhu, Chuqing Sun, Min Li, Guoru Hu, Xing-Ming Zhao*, Wei-Hua Chen*. Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomized controlled trial. Gut, 2024, 73(7):1087-1097.
11. Yucheng T. Yang, Ziquan Gan, Jinglong Zhang, Xingzhong Zhao, Yifan Yang, Shuwen Han, Wei Wu*, Xing-Ming Zhao*. STAB2: an updated spatio-temporal cell atlas of the human and mouse brain. Nucleic Acids Research, 2024, 52(D1):D1033-D1041.
12. Senying Lai, Huarui Wang, Peer Bork*, Wei-Hua Chen*, Xing-Ming Zhao*. Long-read sequencing reveals extensive gut phagenome structural variations driven by genetic exchange with bacterial hosts. Science Advances, 2024, 10(33):eadn3316.
13. Yanqi Dong, Wei-Hua Chen*, Xing-Ming Zhao*.VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes. Genome Biology, 2024, 25(1):177.
14. Celio Dias Santos-Junior, Marcelo D. T. Torres, Yiqian Duan, Alvaro Rodriguez del Rio, Thomas S. B. Schmidt, Hui Chong, Anthony Fullam, Michael Kuhn, Chengkai Zhu, Amy Houseman, Jelena Somborski, Anna Vines, Xing-Ming Zhao, Peer Bork, Jaime Huerta-Cepas, Cesar de la Fuente-Nunez*, Luis Pedro Coelho*. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell, 2024, 187(14):3761-3778.e16.
15. Bo Yuan, Shuqian Zhang, Liting Song, Jinlong Chen, Jixin Cao, Jiayi Qiu, Zilong Qiu, Jingqi Chen*, Xing-Ming Zhao*, Tian-Lin Cheng*. Engineering of cytosine base editors with DNA damage minimization and editing scope diversification. Nucleic Acids Research. 2023, 51(20):e105.
16. Senying Lai, Yan Yan, Yanni Pu, Shuchun Lin, Jian-Ge Qiu, Bing-Hua Jiang, Marisa Isabell Keller, Mingyu Wang, Peer Bork*, Wei-Hua Chen*, Yan Zheng*, Xing-Ming Zhao*. Enterotypes of the human gut mycobiome. Microbiome. 2023, 11(1):179.
17. Xingzhong Zhao, Liting Song, Anyi Yang, Zichao Zhang, Jinglong Zhang, Yucheng T. Yang*, Xing-Ming Zhao*. Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues. Genome Medicine. 2023, 15(1):56.
18. Chuqing Sun, Jingchao Chen, Menglu Jin, Xueyang Zhao, Yun Li, Yanqi Dong, Na Gao, Zhi Liu*, Peer Bork*, Xing-Ming Zhao*, Wei-Hua Chen*. Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases. Advanced Science. 2023, 10(25):e2302159.
19. Zi-Chao Zhang, Xingzhong Zhao, Guiying Dong, Xing-Ming Zhao*. Improving Alzheimer's Disease Diagnosis With Multi-Modal PET Embedding Features by a 3D Multi-Task MLP-Mixer Neural Network. IEEE Journal of Biomedical and Health Informatics. 2023, 27(8):4040-51.
20. Min Li, Jinxin Liu, Jiaying Zhu, Huarui Wang, Chuqing Sun, Na L Gao, Xing-Ming Zhao*, Wei-Hua Chen*. Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers. Gut Microbes. 2023, 15(1):2205386.
21. Yang Gao, Xiaofei Yang, Hao Chen, Xinjiang Tan, Zhaoqing Yang, Lian Deng, Baonan Wang, Shuang Kong, Songyang Li, Yuhang Cui, Chang Lei, Yimin Wang, Yuwen Pan, Sen Ma, Hao Sun, Xiaohan Zhao, Yingbing Shi, Ziyi Yang, Dongdong Wu, Shaoyuan Wu, Xingming Zhao, Binyin Shi, Li Jin, Zhibin Hu, Chinese Pangenome Consortium (CPC), Yan Lu*, Jiayou Chu*, Kai Ye*, Shuhua Xu*. A pangenome reference of 36 Chinese populations. Nature. 2023, 619(7968):112-121.
22. Shuqian Zhang, Liting Song, Bo Yuan, Cheng Zhang, Jixin Cao, Jinlong Chen, Jiayi Qiu, Yilin Tai, Jingqi Chen, Zilong Qiu*, Xing-Ming Zhao*, Tian-Lin Cheng*. TadA reprogramming to generate potent miniature base editors with high precision. Nature Communications. 2023, 14(1):413.
23. Tianjiao Li, Xing-Ming Zhao*, Limin Li*. Co-VAE: Drug-target binding affinity prediction by co-regularized variational autoencoders. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2022, 44(12):8861-8873.
24. Senying Lai, Shaojun Pan, Chuqing Sun, Luis Pedro Coelho*, Wei-Hua Chen*, Xing-Ming Zhao*. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies. Genome Biology, 2022, 23(1):242.
25. Liting Song, Yucheng T Yang, Qihao Guo, ZIB Consortium, Xing-Ming Zhao*. Cellular transcriptional alterations of peripheral blood in Alzheimer’s disease. BMC Medicine, 2022, 20(1):266.
26. Jingqi Chen*, Liting Song, Anyi Yang, Guiying Dong, Xing-Ming Zhao*. Disrupted long-range gene regulations elucidate shared tissue-specific mechanisms of neuropsychiatric disorders. Molecular Psychiatry, 2022, 27(6):2720-2730.
27. Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao*, Luis Pedro Coelho*. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. Nature Communications, 2022, 13(1):2326.
28. Luis Pedro Coelho*, Renato Alves, Alvaro Rodriguez del Rio, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquin Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjorn Nielsen, Jaime Huerta-Cepas*, Peer Bork*. Towards the biogeography of prokaryotic genes. Nature, 2022,601(7892):252-256.
29. Guiying Dong, Jianfeng Feng, Fengzhu Sun, Jingqi Chen*, Xing-Ming Zhao*. A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank. Genome Medicine. 2021, 13(1): 110.
30. Liting Song, Shaojun Pan, Zichao Zhang, Longhao Jia, Wei-Hua Chen*, Xing-Ming Zhao*. STAB: a spatio-temporal cell atlas of the human brain. Nucleic Acids Research, 2021, 49(D1): D1029-1037.
近五年代表性科研项目：
主持科技部国家重点研发计划项目、国家杰出青年基金项目、国自然基金委重点和面上、上海市科委重点等项目十余项。
获奖情况：
上海市生物信息学会杰出贡献奖（2024年）
上海市明珠领军人才（2023年）
吴文俊人工智能自然科学一等奖（2020年，第一完成人）
教育部高等学校科学研究优秀成果（自然类）二等奖（2018年，第一完成人）