基本信息

李明锟  男  博导  中国科学院北京基因组研究所(国家生物信息中心)


电子邮件: limingkun83@163.com


通信地址: 中国科学院北京基因组研究所


邮政编码:

研究领域

1. 新冠病毒基因组变异与进化研究


2. 新冠肺炎患者人体微生物组研究


3. 基于高通量测序数据分析的病原微生物诊断方法开发


4. 人体微生物组(呼吸道、肠道)多样性及其与健康关联研究

招生信息


招生专业
0710Z1-基因组学
0710J3-生物信息学
招生方向
线粒体DNA遗传与变异
人体微生物组学

教育背景

2008-09--2013-02   马克斯普朗克进化人类学研究所   博士
2001-09--2007-07   西北农林科技大学   硕士

工作经历


工作简历
2013-11~2017-11,梅里埃基金会, 课题组长
2013-03~2013-10,马克斯普朗克进化人类学研究所, 博士后
2008-03~2008-08,中国科学院计算生物学研究所, 助理研究员
2007-11~2008-02,中国农业科学院蔬菜花卉研究所, 助理研究员

出版信息

39. Ting Zhang#, Ying Yang#, Zichun Xiang#, Chun-Chun Gao#, Wenjing Wang, Conghui Wang, Xia Xiao, Xing Wang, Wei-Nan Qiu, Wen-Jie Li, Lili Ren, Mingkun Li, Yong-Liang Zhao, Yu-Sheng Chen*, Jianwei Wang*, Yun-Gui Yang*#. N6-methyladenosine regulates RNA abundance of SARS-CoV-2. Cell Discov 7, 7 (2021). 

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

37. 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. Cold-chain food contamination as the possible origin of Covid-19 resurgence in Beijing. 2020. National Science Review. 7(12):1861-2864.

36. Liu Qi #, Zhao SL #, Shi CM #, Song SH #, Zhu SH, Su YK, Zhao WM, Li MK, Bao YM, Xue YB*, Chen H. 2020. Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters. Genomics, Proteomics & Bioinformatics doi: https://doi.org/10.1016/j.gpb.2020.06.001

35. 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. (Cover story)

34. 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, ciaa203, https://doi.org/10.1093/cid/ciaa203 (recommended by F1000)

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

32. Liu J., Li Y., Feng Y., Pan L., Xie Z., Yan Z., Zhang L., Li M., Zhao J., Sun J.*, Hong L.* Patterned progression of gut microbiota associated with necrotizing enterocolitis and late onset sepsis in preterm infants: a prospective study in a Chinese neonatal intensive care unit. PeerJ. 2019,7:e7310

31. Huebner A, Wachsmuth M, Schroeder R, Li M, Eis-huebinger A, Madea B, Stoneking M. 2019. Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome. Scientific Report. 9:11219.

30. 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.

29. Lili Ren#, Rongbao Zhang#, Jian Rao, Yan Xiao, Zhao Zhang, Bin Yang, Depan Cao, Hui Zhong, Pu Ning, Ying Shang, Mingkun Li*, Zhancheng Gao*, Jianwei Wang* 2018. Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status. mSystems. 3(5): e00199-18. Editor's Pick 

28. Li Xianfeng#, Shi, Leisheng#, Wang Yan#, Zhao Xiaolu, Teng Huajing; Shi Xiaohui, Yang Haonan; Ruan Shasha, Li Mingkun,Sun Zhongsheng*, Zhan Qimin*, Mao Fengbiao* 2018.OncoBase: a platform for decoding regulatory somatic mutations in human cancers. Nucleic Acids Res.

27.   D Li, X Du, X Guo, L Zhan, X Li, C Yin, C Chen, Li MK, B Li, H Yang, J Xing. 2017. Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations. Journal of Experimental & Clinical Cancer Research 36 (1), 168

26.   Yan F, Xiao Y, Li M, Zhang H, Zhang R, Zhou H, Shen H, Wang J, Li W, Ren L. 2017, Metagenomic analysis identified human rhinovirus B91 infection in an adult suffered severe pneumonia. Am J Resp Crit Care. 195 (11) :1535

25.   Ren L, Yang D, Ren X, Li M, Mu X, Wang Q, Cao J, Hu K, Yan C, Fan H, Li X, Chen Y, Wang R, An F, An S, Luo M, Wang Y, Xiao Y, Xiang Z, Xiao Y, Li L, Huang F, Jin Q, Gao Z, Wang J. 2017. Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21. Sci Rep. 7: 41601

24.   Li MK, Rothwell R, Vermaat M, Wachsmuth Manja, Schroder R, et al. Genome of the Netherlands Consortium. 2016. Transmission of human mtDNA heteroplasmy in the genome of the Netherlands families: support for a variable-size bottleneck. Genome Research, 26:417-426

23.   Wachsmuth M, Huebner A, Li MK, Madea B, Stoneking M. 2016. Age-related and heteroplasmy-related variation in human mtDNA copy number. Plos Genet, 12(3): e1005939

22.   Li MK, Schroeder R, Ni SY, Madea B, Stoneking M. 2015. Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. PNAS. 112(8):2491-6

21.   The Genome of the Netherlands Consortium. 2014. Whole-genome sequence variation, population structure and demographic history of the Netherlands. Nature Genetics. 46(8):818-25.

20.   Li J, Quinque D, Horz HP, Li MK, Rzhetskaya M, Raff JA, Hayes MG, Stoneking M. 2014. Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa. BMC Microbiology, 14: 316.

19.   Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Santana Sagredo F, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PLF, Li MK, et al. 2014. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology. 24(21):R1035-7

18.  Lippold S, Xu HY, Ko A, Li MK, Renaud G, Butthof A, Schroeder R, Stoneking M. 2014. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investigative Genetics. 5:13

17.  Rieux A, Eriksson A, Li MK, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F. 2014. Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution. 31(10):2780-92

16.  Giuliani C, Barbieri C, Li MK, et al. 2014. Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing. AGING. 6(6):454-67.

15.  Ko AMS, Chen CY, Fu Q, Delfin F, Li MK, et al. 2014. Early Austronesians: into and out of Taiwan. American Journal of Human Genetics. 94(3), 426-436

14.Delfin F, Ko A, Li MK, Gunnarsdottir ED, Tabbada K, Salvador JM, Calcacl GC, Sagum MS, Datar FA, Padilla SG, DeUngria MCA, Soneking M. 2013. Complete mtDNA genomes of Filipino ethnolinguistic groups: A melting pot of recent and ancient lineages in the Asia-Pacific region. European Journal of Human Genetics. doi:10.1038

13.  Li J, NasidzeI, Quinque D, Li MK, Horz HP, Andre C, Garriga RM, Halbwax M, Fischer A, Stoneking M. 2013. The saliva microbiome of Pan and Homo. BMC Microbilogy 13:204

12.  Li MK* and Stoneking M. 2012. A new approach for detecting low-level mutations in next-generation sequence data. Genome Biology, 13:R34. (Corresponding author)

11.  Li MK*, Schroeder R, Ko A, Stoneking M. 2012. Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acid Research, 40:e137 (Corresponding author)

10.  Barbieri C, Whitten M, Beyer K, Schreiber H, Li MK, Pakendorf B. 2012. Contrasting Maternal and Paternal Histories in the Linguistic Context of Burkina Faso. Molecular Biology and Evolution, 29 (4): 1213-1223

9.  Gunnarsdottir E, Li MK, Bauchet M, Finstermeier K, Stoneking M. 2011.High-throughput sequencing of complete human mtDNA genomes from the Philippines.Genome Research, 21(1):1-11

8.  Gunnarsdottir E, Nandineni MR, Li MK, Myles S, Gil D, Pakendorf B, Stoneking M. 2011. Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communication. 2:228

7.  Schoenberg A, Theunert C, Li MK, Stoneking M, Nasidze I. 2011. High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences. European Journal of Human Genetics, 19(9):988-94

6.  Nasidze I, Li J, Schroeder R, Creasey JL, Li MK, Stoneking M. 2011. High diversity of the saliva microbiome in Batwa Pygmies. Plos One, 6(8):e23352

5.  Li MK*, Schoenberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M*. 2010. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. American Journal of Human Genetics. 87(2):237-49. (Corresponding author)

4.  Nasidze I, Quinque D, Li J, Li MK, Tang K, Stoneking M. 2009. Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Analytical Biochemistry. 391(1):64-8

3.  Li MK* and Chen SS. 2011. The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evolutionary Biology. 11:3 (Corresponding author)

2.  Li MK, Gu L, Chen SS, Dai JQ, Tao SH. 2008. Evolution of the isochore structure in the scale of chromosome: insight from the mutation bias and fixation bias. Journal of Evolutionary Biology. 21(1):173-82

1.  Gong X, Fan S, Bilderbeck A, Li MK, Pang H, Tao S. 2008. Comparative analysis of essential genes and nonessential genes in Escherichia coli K12. Molecular Genetics and Genomics. 279(1):87-94


科研经费


科研项目
( 1 ) 抗病毒靶标的生物信息学分析, 参与, 国家级, 2018-01--2020-12
( 2 ) 基于单倍型数据的人类线粒体DNA异质性突变研究, 主持, 国家级, 2019-01--2022-12
( 3 ) 新冠病毒基因组序列的演化分析, 参与, 国家级, 2020-05--2021-06
( 4 ) 生物数据存储管理与交互利用系统, 参与, 部委级, 2020-01--2024-12

指导学生

已指导学生

夏瑞燕  硕士研究生  0710Z1-基因组学  

现指导学生

康露  硕士研究生  0710J3-生物信息学  

沈子杰  硕士研究生  0710Z1-基因组学  

史雷胜  博士研究生  0710J3-生物信息学  

杨景  硕士研究生  0710J3-生物信息学  

马文泰  硕士研究生  0710J3-生物信息学  

钟嘉鑫  博士研究生  0710J3-生物信息学  

王淳  博士研究生  0710J3-生物信息学  

张林峰  硕士研究生  0710Z1-基因组学  

朱荣辉  硕士研究生  0710Z1-基因组学  

符豪毅  博士研究生  0710J3-生物信息学