细菌重金属与耐药基因共抗性及其耐药进化机制研究；
微生物基因组学 (基因组及比较基因组分析,细菌NGS数据分析)；
基因组序列大数据可视化方法研究

1. 国家自然科学基金（地区基金项目）、21966015、重金属Ag胁迫土壤中细菌群落多样性及其耐药响应研究、2020/01-2023/12、64.5万（含学校配套）、主持、在研
2. 国家自然科学基金（青年基金项目）、21507012、环境中亚致死（Sublethal）剂量重金属诱导耐药菌形成及扩散机制研究、2016/01-2018/12、20万、主持、已结题
3. 中国博士后科学基金面上项目（一等资助）、2015M570329、环境中低剂量重金属促进细菌耐药性扩散机制研究、2015/05-2016/11、8万、主持、已结题
4. 贵州省科技厅联合基金、黔科合LH字[2017]7176、比较基因组解析斯氏假单胞菌进化及适应机制、2017/05-2019/05、6万、主持、在研
5. 贵州省科学技术基金项目、黔科合基础[2019]1287、黔东南州地区大气颗粒物中病原微生物群落结构及相关耐药机制研究、2019/01-2021/12、17.5万（含学校配套）、主持、在研
6. 贵州省教育厅自然科学研究-拔尖人才项目、黔教合KY[2020]043、基于细菌基因组序列大数据研究细菌重金属抗性基因与耐药基因共分布特征、2020/10-2023/10、30万（含学校配套）、主持 、在研
7. 贵州省教育厅自然科学研究-重点项目、黔教合KY[2015]395 、2015/11-2018/11、10万（含学校配套）、主持、已结题
8. 国家自然科学基金委重大研究计培育项目、91643106、大气细颗粒物毒性组分对呼吸道病原菌耐药性的影响机制研究、2017/01-2019/12、参加、已结题
9. 国家自然科学基金面上项目、31170106、嗜砷性砷氧化细菌砷代替磷的分子机制、2012/01-2014/12、参加、已结题
10. 国家自然科学基金重大国际合作项目、31010103903、化能异养型和自养型亚砷酸氧化菌的砷感应与表达调控分子机理、2011/01-2013/12、参加、已结题â
11. 国家自然科学基金面上项目、30970075、亚砷酸氧化菌对砷的感应与信号转导机制研究、2010/01-2012/12、参加、已结题

1. Li X*, Yang Z, Zhang G, Si S, Wu X, Cai L*. Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria. Genes 2022, 13(11):2149, https://doi.org/10.3390/genes13112149. (SCI收录, IF=4.14). *Corresponding author
2. Li X*, Yang Z, Wang Z, Li W, Zhang G, Yan H. Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity. Frontiers in Microbiology 2022, DOI: 10.3389/fmicb.2021.755874. (SCI收录, IF=5.64). *Corresponding author
3. Li X*, Chen F, Chen Y. Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes, Bioinformatics 2020, 36(12): 3871-3873. (SCI收录, IF=5.61), *Corresponding author
4. Li X, April Z. Gu, Zhang Y, Xie B, Li D, Chen J. Sub-lethal Concentrations of Heavy Metals Induce Antibiotic Resistance via Mutagenesis. Journal of Hazardous Materials 2019, 369:9–16, https://doi.org/10.1016/j.jhazmat.2019.02.006. (SCI收录, IF=6.43)
5. Li X, Zhang L, Wang G. Genomic evidence reveals extreme diversity and wide distribution of the arsenic-related genes in Burkholderiales. PLoS ONE, 2014, 9(3): e92236. (SCI收录, IF=3.73)
6. Li X, Hu Y, Gong J, Zhang L, Wang G. Comparative genome characterization of Achromobacter members reveals potential genetic determinants facilitating the adaptation to a pathogenic lifestyle. Appl Microbiol Biotechnol, 2013, 97(14):6413-6425. (SCI收录, IF=3.68)
7. Zhang L*, Li X*, Zhang F, Wang G. Genomic analysis of Agrobacterium radiobacter DSM 30147T and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993.Stand. Genomic Sci.2013, 9:574-84. (*: ¹²Í¬µÚÒ»×÷Õß). (SCI收录, IF=2.01)
8. Li X, Gong J, Hu Y, Cai L, Johnstone L, Grass G, Rensing C, Wang G. Genome sequence of the moderately halotolerant, arsenite-oxidizing bacterium Pseudomonas stutzeri TS44. J. Bacteriol, 2012, 194(16):4473-4. (Genome Announcements) (SCI收录, IF=3.83)
9. Li X, Hu Y, Gong J, Lin Y, Johnstone L, Rensing C, Wang G. Genome sequence of the highly efficient arsenite-oxidizing bacterium Achromobacter arsenitoxydans SY8. J. Bacteriol, 2012, 194(5):1243-4. (Genome Announcements) (SCI收录, IF=3.83)
10. He M, Li X, Liu H, Miller SJ, Wang G and Rensing C. Characterization and genomic analysis of a highly chromate resistant and reducing bacterial strain Lysinibacillus fusiformis ZC1. J Hazard Mater, 2011, 185:682-8. (SCI收录, IF=4.14)
11. He M, Li X, Guo L, Miller SJ, Rensing C and Wang G. Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1. BMC Microbiol, 2010, 10:221. (SCI收录, IF=2.89)
12. Cai L, Rensing C, Li X, Wang G. Novel gene clusters involved in arsenite oxidation and resistance in two arsenite oxidizers: Achromobacter sp. SY8 and Pseudomonas sp. TS44. Appl Microbiol Biotechnol, 2009, 83(4):715-25. (SCI收录, IF=2.54)
13.Ye Zhang, April Z.Gu, Tianyu Cen, Xiangyang Li, Miao He, Dan Li, Jianmin Chen. Sub-inhibitory concentrations of heavy metals facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes in water environment.Environmental Pollution, 2018,237:74-82.
14.Ye Zhang, April Z. Gu, Tianyu Cen, Xiangyang Li, Dan Li,Jianmin Chen. Petrol and diesel exhaust particles accelerate the horizontal transfer of plasmid-mediated antimicrobial resistance genes.Environment International, 2018, 114:280-287.
15.Ye Zhang, April Z. Gu, Shanshan Xie, Xiangyang Li, Tianyu Cen, Dan Li, Jianmin Chen, Nano-metal oxides induce antimicrobial resistance via radical-mediated mutagenesis. Environment International, 2018, 121(2): 1162-1171.
16.Qian Wang, Wentao Zhu, Entao Wang, Linshuang Zhang, Xiangyang Li, Gejiao Wang.Genomic identification of rhizobia-related strains and threshold of ANI and core-genome for family, genus and species. International Journal of Environmental & Agriculture Research, 2(6):76-86.
17. Li X, Zou X, Zhang K, Meng H, Shi D.2018. Draft genome sequence of Pseudomonas sp. LS-2, isolated from a diseased Gastrodiaelata plant. Microbiol Resour Announc, 2018, 7:e01342-18. doi.org/10.1128/MRA.01342-18.
18. 李向阳, 汤宏, 张国辉. 比较基因组分析斯氏假单胞菌遗传多样性及固氮基因岛进化机制. 江苏农业科学, 2017年1月.