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空格围绕纤毛虫原生动物的多样性与系统演化、细胞结构的发生与分化、表观遗传调控、性别决定、基因组重排、基因进化等基础科学问题，主要研究包括：

（1）聚焦我国温带、亚热带-热带沿海与内陆湿地环境中的自由生活类群，研究其区系、形态分类、物种多样性、群落结构、生态学功能与地位、时空与地理分布；

（2）以四膜虫为材料，探讨以甲基化修饰为主的表观遗传信息对基因表达和复制的调控机制；

（3）以游仆虫、草履虫等为材料，探讨纤毛虫有性生殖过程中大、小核发育、分化及基因组重排的模式和机制，解析其性别分化和决定的相关基因及分子机制；

（4）围绕纤毛虫的系统演化、分化过程中的重要事件和组学特征，探讨细胞及胞器分化、适应与进化、结构与功能关系等重要现象和过程中相关功能基因的调控机制；

（5）以草履虫为材料，聚焦胞质分裂调控的分子机制，探究收缩环的形成、细胞极性的建立和维持；

（6）探讨纤毛虫无性及有性生殖期间细胞器结构及模式的形成、分化等个体发育特征；

（7）构建纤毛虫各代表类群的DNA库、标记基因库、组学信息库等遗传信息库; 探讨纤毛门内各高阶阶元间的亲缘关系、系统发育与演化。

空Focusing on fundamental research related to ciliated protozoa, including biodiversity and phylogeny, morphogenesis and differentiation of subcellular structures, epigenetic regulation, sex determination, genomics and genome rearrangement, gene evolution, etc. Our current focuses are:

空(1) Taxonomy and biodiversity. Focusing on free-living ciliates in coastal and inland wetlands across temperate and subtropical-tropical regions in China, explore their fauna, morphological classification, species diversity, community structure, ecological functions, and spatiotemporal and geographical distributions.

空(2) Epigenetics. Understand how DNA and histone methylations affect gene expression and DNA replication by using the model ciliate Tetrahymena thermophila.

空(3) Genome rearrangement and sex determination. Investigate the patterns and mechanisms of nucleus development, differentiation, and genome rearrangements during sexual reproduction in representative ciliates, and explore the evolution and molecular mechanisms of sex determination, using Euplotes and Paramecium as model organisms.

空(4) Genome evolution. Explore the regulatory mechanisms of functional genes involved in key phenomena and processes of ciliates, such as cell and organelle differentiation, speciation and adaptation, applying combined multi-omics methods.

空(5) Cytokinesis. Using Paramecium as model organism, focus on the molecular mechanism of cytokinesis regulation, including the contractile ring formation, and the establishment and maintenance of cell polarity.

空(6) Cell development. Focus on the formation, differentiation, and developmental characteristics of organelle structures and patterns during sexual and asexual reproduction in ciliates.

空(7) Phylogenetics and systematics. Investigate the phylogeny, systematics, and evolutionary relationships among diverse lineages within the phylum Ciliophora, while constructing genetic information databases containing genomic DNA, marker gene sequences and omics data for representative ciliate groups.