CAS Center for Excellence in Animal Evolution and Genetics

Li Mingkun

2018-10-24 | | 【Print】

From 2008 to 2013, Dr. LI Mingkun studied in Max Planck Institute for Evolutionary Anthropology for Bioinformatics, and he was a Postdoc at Max Planck Institute for Evolutionary. Anthropology from Mar 2013-Oct 2013 Postdoc at Max Planck Institute for Evolutionary. Anthropology.

Work experience

Jan 2018-Present Professor and principal investigator at Beijing Institute of Genomics, Chinese Academy of Sciences.

Nov 2013-Dec 2017 Senior Scientist/Bioinformatics Group Leader at Fondation Merieux

Research field

His major research interests are genetics of mitochondrial DNA and human lung microbiome.

“Genetic variation analysis of human mitochondrial DNA based on haplotype data” funded by NSFC.

Research Interest

1) Genetics of Mitochondrial DNA.
Mitochondrion has its own genomic DNA(mtDNA), that has thousands copies in each cell. It is 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 are normally in heteroplasmic states, 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.

2) 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 alters 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? etc.

Selected Publications

1. Yan F, Xiao Y, Li MK, Zhang H, Zhang R, Zhou H, Shen H, Wang J, Li W, Ren L. Metagenomic analysis identified human rhinovirus B91 infection in an adult suffered severe pneumonia. American Journal of Respiratory and Critical Care Medicine, 2017, 195 (11) :1535.

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

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

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

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

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

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

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

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

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