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

方向1: 病原微生物的精准检测技术

方向2: 人体微生物组特征及其与营养、疾病关联

方向3: 智能化基因组变异演化分析技术

招生信息

欢迎生物信息学、数学、遗传学、生物化学与分子生物学、微生物学同学报考及前来实习工作。

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

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

2013-11~2017-12,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

社会兼职
2022-11-30-今,中国医疗保健国际交流促进会临床微生物学分会, 常务委员
2021-09-11-今,THE WESTERN PACIFIC REGION MERGING MOLECULAR PATHOGEN CHARACTERIZATION TECHNOLOGIES (EMPACT) SURVEILLANCE NETWORK, Temporary Advisor
2021-05-26-今,中华预防医学会生物信息学分会, 常务委员

教授课程

精准医学概论

出版信息

54. Liu Z#, Gao X#, Kan C#, Li L, Zhang Y, Gao Y, Zhang S, Zhou L, Zhao H, Li MK*, Zhang Z*, Sun Y*. CRISPR-Cas13d effectively targets SARS-CoV-2 variants, including Delta and Omicron, and inhibits viral infection. (2023). MedComm, https://doi.org/10.1002/mco2.208.

53. 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. https://doi.org/10.1016/j.bsheal.2022.10.004

52. Chen S, Wei Y*, Yue X, Xu K, Li MK, Lin W. Correlation analysis between the occurrence of epidemic in ancient China and solar activity (2023). Science China Earth Sciences 66:161–168 

51. Sun X, Kan CW, Ma WT, Du ZL*, Li MK*. Genomic analysis of the suspicious SARS-CoV-2 sequences in the public sequencing database (2023). Microbiology Spectrum. https://doi.org/10.1128/spectrum.03426-22

50. Feng XL, Yu DD, Zhang M, Li XH, Zou QC, Ma WT, Han JB, Xu L, Yang CX, Qu W, Deng ZH, Long JY, Long YHP, Li MK, Yao YG, Dong XQ, Zeng JX, Li MH*. Characteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates (2022). Virologica Sinica. https://doi.org/10.1016/j.virs.2022.09.007

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

48. Liu Q#, Iqbal MF#, Yaqub T, Firyal S, Zhao YQ*, Stoneking M*, Li MK*. The Transmission of Human Mitochondrial DNA in Four-Generation Pedigrees (2022). Human Mutation. https://doi.org/10.1002/humu.24390. (Cover)

47. 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*. Possible recombination between two variants of concern in a COVID-19 patient (2022) . Emerging Microbes & Infections. 11(1):552-555.

46. Ma WT#, Yang J#, Fu HY, Su C, Yu CX, Wang QH, de Vasconcelos ATR, Bazykin G, Bao YM, Li MK*. Genomic perspectives on the emerging SARS-CoV-2 omicron variant. (2021), Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2022.01.001

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

44. Wu CI*, Wen H, Lu J, Su X, Hughes AC, Zhai W, Chen C, Chen H, Li M, Song S, Qian Z, Wang Q, Chen B, Guo Z, Ruan Y, Lu X, Wei F, Jin L, Kang L, Xue Y, Zhao G, Zhang YP (2021) On the origin of SARS-CoV-2—The blind watchmaker argument. Science China Life Sciences. 64: 1560–1563.

43. Wu Z, Jin Q, Wu G, Lu J, Li M, Guo D, Lan K, Feng L, Qian Z, Ren L, Tan W, Xu W, Yang W, Wang J*, Wang C (2021) SARS-CoV-2's origin should be investigated worldwide for pandemic prevention. 2021.The Lancet. DOI: 10.1016/S0140-6736(21)02020-1 .

42. 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.

41. 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*. Genomic Epidemiology of SARS-CoV-2 in Pakistan. (2021). Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2021.08.007.

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

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. 2020. Clinical Infectious Diseases, 71(15):713-720. (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, 国家任务, 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, 负责人, 国家任务, 2019-01--2022-12
( 3 ) 新冠病毒基因组序列的演化分析, 参与, 国家任务, 2020-05--2021-06
( 4 ) 生物数据存储管理与交互利用系统, 参与, 中国科学院计划, 2020-01--2024-12
( 5 ) 金砖五国新冠病毒基因组变异监测, 负责人, 国家任务, 2021-01--2022-12
( 6 ) 北京市重点呼吸道传染病分子溯源技术研究及应用, 参与, 地方任务, 2021-01--2021-12

指导学生

已指导学生

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  

夏瑞燕  硕士研究生  0710Z1-基因组学  

现指导学生

史雷胜  博士研究生  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  

孙潇  硕士研究生  0710J3-生物信息学  

阚传雯  硕士研究生  0710Z1-基因组学  

马文泰  博士研究生  0710J3-生物信息学  

姜旋  博士研究生  0710J3-生物信息学  

申佩瑶  硕士研究生  0710Z1-基因组学  

杨景  博士研究生  0710J3-生物信息学  

张昊  硕士研究生  0710J3-生物信息学  

张恺文  硕士研究生  0710J3-生物信息学  

纪小桐  硕士研究生  0710J3-生物信息学