方向1：人体微生物组成与功能研究。研究人体微生物组（呼吸、肠道、肿瘤）组成及变化规律，及其与疾病发生、发展及预后的关联，发现疾病新型分子标志物，揭示人体微生物组形成与变化的驱动力。

方向2：临床宏基因组技术研发。开发基于高通量测序数据分析的微生物及病原微生物分析鉴定方法，建立快速、灵敏、准确的病原体筛查鉴定系统，开发病原微生物风险评估体系。

方向3：智能化基因组变异演化分析。主要围绕新冠病毒基因组开展分子演化分析、人工智能预测，建立病原体流行规律及演化趋势分析预测体系。

1. 生物数据存储管理与交互利用系统，参与，2020-2024，在研

2. 上呼吸道微生物组稳定性的纵向研究，主持，2023-2025，在研

3. 呼吸道微生物的宏基因组检测方法学研究，主持，2022-2024，在研

4. 呼吸道微生物组特征及在呼吸道感染中免疫调控机制研究，主持，2022-2027，在研

近五年代表性成果：

1. Wentai Ma#, Haoyi Fu#, Fanchong Jian, Yunlong Cao*, Mingkun Li*. (2024). Distinct SARS-CoV-2 populational immune backgrounds tolerate divergent RBD evolutionary preferences. National Science Review. https://doi.org/10.1093/nsr/nwae196. 

2. Wentai Ma, Haoyi Fu, Fanchong Jian, Yunlong Cao*, Mingkun Li* (2023). Immune evasion and ACE2 binding affinity contribute to SARS-CoV-2 evolution. Nature Ecology & Evolution, 7(9):1457-1466.

3. Lili Ren#, Yeming Wang#, Jiaxin Zhong#, Xia Li , Yan Xiao , Jie Li , Jing Yang , Guohui Fan , Li Guo ; Zijie Shen , Lu Kang , Leisheng Shi , Qiong Li , Jizhou Li , Lin Di , Haibo Li , Conghui Wang , Ying Wang , Xinming Wang , Xiaohui Zou , Jian Rao , Li Zhang , Jianbin Wang , Yanyi Huang , Bin Cao*, Jianwei Wang*, Mingkun Li*. Dynamics of the Upper Respiratory Tract Microbiota and its Association with Mortality in COVID-19. 2021. American Journal of Respiratory and Critical Care Medicine. 204(12):1379-1390.

4. Zhuo Zhou#, Lili Ren#, Li Zhang#, Jiaxin Zhong#, Yan Xiao#, Zhilong Jia, Li Guo, Jing Yang, Chun Wang, Shuai Jiang, Donghong Yang, Guoliang Zhang, Hongru Li, Fuhui Chen, Yu Xu, Mingwei Chen, Zhancheng Gao, Jian Yang, Jie Dong, Bo Liu, Xiannian Zhang, Weidong Wang, Kunlun He, Qi Jin, Mingkun Li*, Jianwei Wang*. Heightened innate immune responses in the respiratory tract of COVID-19 patients. 2020. Cell Host & Microbe, 27(6): 883-890.

5. Zijie Shen#, Yan Xiao#, Lu Kang#, Wentai Ma#, Leisheng Shi, Li Zhang, Zhuo Zhou, Jing Yang, Jiaxin Zhong, Donghong Yang, Li Guo, Guoliang Zhang, Hongru Li, Yu Xu, Mingwei Chen, Zhancheng Gao, Jianwei Wang, Lili Ren*, Mingkun Li*. Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients, Clinical Infectious Diseases, 2020, 71:713-720.

近五年其他成果：

1. Jing Yang#, Jinman Li#, Linfeng Zhang#, Zijie Shen, Yan Xiao, Guoliang Zhang, Mingwei Chen, Fuhui Chen, Ling Liu, Ying Wang, Lan Chen, Xinming Wang, Li Zhang, Lu Wang, Zhang Wang, Jianwei Wang*, Mingkun Li*, Lili Ren*. (2024). Highly diverse sputum microbiota correlates with the disease severity in patients with community-acquired pneumonia: a longitudinal cohort study. Respiratory Research. 25:223.

2. Jiaxin Zhong#, Li Guo#, Yeming Wang#, Xuan Jiang, Chun Wang, Yan Xiao, Ying Wang, Fei Zhou, Chao Wu, Lan Chen, Xinming Wang, Jianwei Wang, Bin Cao*, Mingkun Li*, LiLi Ren*. (2024). Gut Microbiota Improves Prognostic Prediction in Critically Ill COVID-19 Patients alongside Immunological and Hematological indicators. Research. 7:0389.

3. Liandong Li, Haoyi Fu, Wentai Ma, Mingkun Li∗. (2024). PySNV for complex intra-host variation detection. Bioinformatics. 40(3):btae116.

4. Xun Wang#, Shujun Jiang#, Wentai Ma#, Xiangnan Li, Kaifeng Wei, Faren Xie, Chaoyue Zhao, Xiaoyu Zhao, Chen Li, Rui Qiao, Yuchen Cui, Yanjia Chen, Jiayan Li, Guonan Cai, Changyi Liu, Jizhen Yu, Jixi Li, Zixin Hu, Wenhong Zhang, Shibo Jiang, Mingkun Li*, Yanliang Zhang*, and Pengfei Wang*. (2024). Enhanced neutralization of SARS-CoV-2 XBB sub-lineages and BA.2.86 by a tetravalent COVID-19 vaccine booster. Cell Host Microbe. 32:25-34

5. Jing Lu#, Li Zhang#, Hao Zhang, Yutao Chen, Jianxin Zhao, Wei Chen, Wenwei Lu*, Mingkun Li*.(2023). Population-Level Variation in Gut Bifidobacterial Composition and Association with Geography, Age, Ethnicity, and Staple Food. npj Biofilms and Microbiomes. 9:98

6. Wentai Ma#，Leisheng Shi#，Mingkun Li*. (2023). A fast and accurate method for SARS-CoV-2 genomic tracing. Briefings in Bioinformatics. 24(6):bbad339

7. Liu Z#, Gao X#, Kan C#, Li L, Zhang Y, Gao Y, Zhang S, Zhou L, Zhao H, Li MK*, Zhang Z*, Sun Y*. (2023). CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection. MedComm, 4(1):e208

8. He Y#, Dang S#, Ma W#, Chen L, Zhang R, Mei S, Wei X, Lv Q, Peng B, Sun Y, Kong D, Chen J, Li S, Tang X, Lu Q, Zhu C, Chen Z, Wan J, Zou X, Li MK*, Feng T*, Ren L*, Wang J. Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft. (2023). Biosafety and Health. 5(1):62-67.

9. Sun X, Kan CW, Ma WT, Du ZL*, Li MK*. (2023). Genomic analysis of the suspicious SARS-CoV-2 sequences in the public sequencing database. Microbiology Spectrum. 11: e03426-22

10. Wang Chun#, Zhang Li#*, Jiang Xuan, Ma Wentai, Geng Hui, Wang X, Li MK*. (2022). Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods. BMC Biology. 20:225.

11. Liu Q#, Iqbal MF#, Yaqub T, Firyal S, Zhao YQ*, Stoneking M*, Li MK*. (2022). The Transmission of Human Mitochondrial DNA in Four-Generation Pedigrees. Human Mutation. 43:1259-1267. 

12. He YQ#, Ma WT#, Dang SY#, Chen L, Zhang RL, Mei SJ, Wei XY, Lv QY, Peng B, Chen JC, Kong DF, Sun Y, Tang XJ, Wu WH, Chen ZG, Li SM, Wan J, Zou X, Li MK*, Feng TJ*, Ren LL*, Wang JW*. (2022). Possible recombination between two variants of concern in a COVID-19 patient. Emerging Microbes & Infections. 11(1):552-555.

13. Ma WT#, Yang J#, Fu HY, Su C, Yu CX, Wang QH, de Vasconcelos ATR, Bazykin G, Bao YM, Li MK*. (2021). Genomic perspectives on the emerging SARS-CoV-2 omicron variant. Genomics, Proteomics & Bioinformatics. 20:60-69.

14. Zhao XL#, Shi LS#, Ruan SS#, Bi WJ, Chen YF, Chen L, Liu YF, Li MK*, Qiao J*, Mao FB*. (2021). CircleBase: an integrated resource and analysis platform for human eccDNAs. Nucleic Acids Research. 50(D1):D72-D78.

15. Shuhui Song#, Cuiping Li#, Lu Kang#, Dongmei Tian#, Nazish Badar#, Wentai Ma, Shilei Zhao, Xuan Jiang, Chun Wang, Yongqiao Sun, Wenjie Li, Meng Lei, Shuangli Li, Qiuhui Qi, Aamer Ikram, Muhammad Salman, Massab Umair, Huma Shireen, Fatima Batool, Bing Zhang, Hua Chen, Yungui Yang, Amir Ali Abbasi*, Mingkun Li*, Yongbiao Xue*, Yiming Bao*. (2021). Genomic Epidemiology of SARS-CoV-2 in Pakistan. Genomics, Proteomics & Bioinformatics. 19:727-740.

16. Jing Lu#, Li Zhang#, Qixiao Zhai, Jianxin Zhao, Hao Zhang, Yuan-Kun Lee, Wenwei Lu*, Mingkun Li*, Wei Chen*. (2021). Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization. npj Biofilms and Microbiomes. 7: 71.

17. Yi Xu#, Lu Kang#, Zijie Shen#, Xufang Li#, Weili Wu, Wentai Ma, Chunxiao Fang, Fengxia Yang, Xuan Jiang, Sitang Gong*,Li Zhang*, Mingkun Li*. (2020). Dynamics of SARS-CoV-2 genome variants in the feces during convalescence. Journal of Genetics and Genomics. 47(10):610-617.

18. Xinghuo Pang#, Lili Ren#, Shuangsheng Wu#, Wentai Ma#, Jian Yang, Lin Di, Jie Li, Yan Xiao, Lu Kang, Shichang Du, Jing Du, Jing Wang, Gang Li, Shuguang Zhai, Lijuan Chen, Wenxiong Zhou, Shengjie Lai, Lei Gao, Yang Pan*, Quanyi Wang*, Mingkun Li*, Jianbin Wang*, Yanyi Huang*, Jianwei Wang*, COVID-19 Field Response Group, COVID-19 Laboratory Testing Group. (2020). Cold-chain food contamination as the possible origin of Covid-19 resurgence in Beijing. National Science Review. 7(12):1861-2864.

19. Liu Q.#, Lin D.#, Li Mingkun.*, Gu Z.* & Zhao Y.* (2019). Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma. Genome Biology and Evolution. 2019,11:2909-2916.

20. Yan Xiao, Li Zhang, Bin Yang, Mingkun Li*, Lili Ren*, Jianwei Wang. (2019). Application of next generation sequencing technology on contamination monitoring in microbiology laboratory. Biosafety & health. 1(1):25-31.