Who we are?

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I am currently hold a position as Senior Scientist/Bioinformatics Group Leader at Fondation Merieux. Meanwhile, I am setting up my own lab at Beijing Institute of Genomics, Chinese Academy of Sciences. My lab is mainly focusing on two topics:.

1. lung microbiome
The lung is relatively sterile compared to the gut; however, the importance of the lung microbiome in health has been well recognized. Alternation of the lung microbiome has been associated with clinical and inflammatory features of several respiratory tract diseases, thus making it a potential target for novel diagnostic and therapeutic approaches. However, the baseline of the lung microbiome is still largely unclear, especially for non-Caucasian populations. Our group is trying to answer the following questions:
What is the core microbiome in the lung?
How the lung microbiome alter during infection?
How microbiome differs between lower respiratory tract and upper respiratory tract?
How microbiome interacts with the host gene expression?
How the viral genome evolves after infecting human?
We are collaborating with Chinese Academy of Medical Sciences and many other hospitals on this work.

2. Mitochondrial DNA
Mitochondrion has its own genomic DNA(mtDNA), that has thousands copies in each cell. Its mutation rate is about 10 times higher than that of nuclear DNA and very few recombinations were observed on mtDNA(maternal inherited), thus making it a frequently-used molecular biomarker in population genetics studies. Meanwhile, mtDNA mutations are known to be associated with several inherited diseases, and these pathogenic mutations as well as other "neutral" mutations are normally in heteroplasmic states (a mixture of wild type and mutant type), which is hard to be detected by ordinary method. With the development of Next-generation Sequencing, it is feasible to identify many low-level heteroplasmies, thus enable us to reexamine the fundamental theory of mtDNA inheritance, including:
Whether paternal leakage exists during mtDNA inheritance?
Whether recombination occurs on mtDNA?
Whether the mtDNA mutation pattern differs between cell line and fresh tissue?
We are collaborating with Max Planck Institute and Genome of the Netherlands consortium on this work.

Besides these two topics, I am also intereted in many other topics, including tumor somatic mutations, fetal DNA in the blood of pregnant women.

Our lab is recruiting staffs, postdocs and students, preferentially with the background of bioinformatics and genomics.


2008-2012 Max Planck Institue for Evolutionary Anthropology, Leipzig, Germany. Bioinformatics
2001-2007 Northwest A & F University,Yangling,China Joint undergraduate-postgraduate program, The National Base of Life Science and Techonology Education
2004-2007 Northwest A & F University,Yangling,China Master, Molecular biology and biochemistry.
2001-2004 Northwest A & F University,Yangling,China Bachelor, Biology.

Working experience

Nov 2013-Nov 2017 Senior Scientist/Bioinformatics Group Leader at Fondation Merieux
Sep 2012-Oct 2013 Postdoc at Max Planck Institute for Evolutionary Anthropology
Mar 2008-Aug 2008 CAS-MPG partner institute for computational biology, Shanghai, Staff Scientist
Nov 2007-Feb 2008 The institute of vegetables and flowers CAAS, (BGI)Beijing, Bioinformatician
Jul 2007-Sep 2007 CAS-MPG partner institute for computational biology, Shanghai, Intern


Human mtDNA genomics and population genetics
1. 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, 10.1101/gr.203216.115
2. 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
3. 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
4 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.
5. 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
6. 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
7. 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
8. 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.
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
Low-level mutation detection (Algorithm development)
15. 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)
16. 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)
17. 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)
18. 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
19. 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): 1535–1536
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.
21. 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
22. 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
23. 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
Molecular evolution
24. Li MK* and Chen SS. 2011. The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evolutionary Biology. 11:3 (Corresponding author)
25. 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
26. 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

Conferences and workshops

2nd Beyond the Genome, 2011, Washington DC, US. Best Poster Prize.
German Gen-AG 'Evolutionary Genetics',2010, Ploen, Germany. Oral presentation.
Asian-Pacific Conference of Tumor Biology and Medicine, 2013, Shijiazhuang, China, plenary talk.
The Sixth National Conference on Bioinformatics and Systems Biology, 2015, Nanjing, China, oral presentation.


Chinese Government Scholarship for Outstanding Self-financed Students Studying Abroad,2011
1000 Talent Yong, 2017