李明錕

2008-09--2013-02 馬克斯普朗克進化人類學研究所 博士

2001-09--2007-07 西北農林科技大學 碩士

2013-11~2017-12,梅里埃基金會, 課題組長

2013-03~2013-10,馬克斯普朗克進化人類學研究所, 博士後

2008-03~2008-08,中國科學院計算生物學研究所, 助理研究員

2007-11~2008-02,中國農業科學院蔬菜花卉研究所, 助理研究員

47. Yaqing He#, Wentai Ma#, Shengyuan Dang#, Long Chen, Renli Zhang, Shujiang Mei, Xinyi Wei, Qiuying Lv, Bo Peng, Jiancheng Chen, Dongfeng Kong, Ying Sun, Xiujuan Tang, Weihua Wu, Zhigao Chen, Shimin Li, Jia Wan, Xuan Zou, Mingkun Li*, Tiejian Feng*, Lili Ren*, Jianwei Wang*. Possible recombination between two variants of concern in a COVID-19 patient (2022) . Emerging Microbes & Infections. https://doi.org/10.1080/22221751.2022.2032375

46. Wentai Ma#, Jing Yang#, Haoyi Fu, Chao Su, Caixia Yu, Qihui Wang, Ana Tereza Ribeiro de Vasconcelos, Georgii A.Bazykin, YimingBao, Mingkun Li*. 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. Xiaolu Zhao#, Leisheng Shi#, Shasha Ruan#, Wenjian Bi, Yifan Chen, Lin Chen, Yifan Liu, Mingkun Li*, Jie Qiao*, Fengbiao Mao* CircleBase: an integrated resource and analysis platform for human eccDNAs. Nucleic Acids Research. (2021). https://doi.org/10.1093/nar/gkab1104

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

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