1.建立以单倍型为单位的线粒体DNA研究新方法 

经典遗传学认为线粒体DNA为母系遗传且不会发生重组，而已有数据并不完全支持这种理论。我们正在开发基于二代+三代测序数据的以单倍型为单位的线粒体DNA数据分析流程，通过分析线粒体DNA单倍型遗传规律，计算父系遗漏及重组发生的概率。此外，我们发现部分线粒体DNA存在复杂的插入缺失现象，目前正使用基于单倍型的方法来完成大规模的复杂插入缺失扫描，对此类突变进行全位的分析解读。 

2.呼吸道微生物组的解析及多组学数据的整合分析 

呼吸道感染是威胁人类健康的重要疾病，近年研究发现，部分致病菌可作为定植菌广泛存在于“正常人”的呼吸道内，与疾病的发生密切相关。本课题组基于宏基因组/转录组数据分析，揭示呼吸道微生物组成及其关键功能元件。同时整合宿主转录组、代谢组等相关数据集，分析呼吸道微生物代谢产物及其对宿主基因表达及代谢和信号通路的影响，从而揭示呼吸道微生物功能。

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. 

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. 

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. 

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. 

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. 

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) 

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. 

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

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. 

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.