以原生动物尤其是纤毛虫为对象，开展系统学、基因组学和进化生物学研究，并致力于建立和开发原生动物基因工程技术。 

1、原生动物生物系统学--在对原生动物主要类群代表种和自由生/寄生/互利共生代表种鉴定和分类的基础上，通过建立原生动物实验生物学、组学尤其是单细胞组学技术和生物信息学分析平台，结合形态、组学及基因功能等多维数据，开展生物系统学研究，理解原生动物生物多样性及其形成机制，并逐步建立起原生动物资源信息库。 

2、原生动物进化与生态功能基因组学--以原生动物纤毛虫为主要对象，发展以四膜虫为主的多种纤毛虫研究模型，在不同分类水平（纲/目/科/属/种群），系统开展比较基因组学、表观基因组学、群体基因组学和实验进化基因组学研究，理解单细胞原生动物适应性进化/生态适应的功能基础，并针对性别决定和生殖进化等基础的进化生物学问题进行深入研究。 

3、原生动物基因工程技术--以四膜虫为主，并逐步开发不同单细胞原生动物基因工程模型，在建立分子遗传操作技术、高效表达技术和培养/发酵技术的基础上，鉴定并利用原生动物中重要的基因资源，研发用于环境污染物监测/降解和农业病害防治的新技术和新策略。

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2.   Feng LF, Wang GY, Hamilton EP, Xiong J, Yan GX, Chen K, Chen X, Dui W, Plemens A, Khadr L, Dhanekula A, Juma M, Dang HQ, Kapler GM, Orias E,Miao W*, Liu YF*. 2017. A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement.Nucleic Acids Research, 45:9481-9502. 

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6.   Xiong J, Lu YM, Feng JM, Yuan DX, Tian M, Chang Y, Fu CJ, Wang GY, Zeng HH*,Miao W*. 2013. Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics.Database-Oxford, bat008. 

7.   Gao S, Xiong J, Zhang CC, Berquist BR, Yang RD, Zhao M, Molascon AJ, Kwiatkowski SY, Yuan DX, Qin ZH, Wen JF, Kapler GM, Andrews PC,Miao W*, Liu YF*. 2013. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation.Genes & Development,27:1662-1679. 

8.   Cervantes MD, Hamilton EP, Xiong J, Lawson MJ, Yuan DX, Hadjithomas M,Miao W*, Orias E. 2013. Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila.Plos Biology,11(3): e1001518. 

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