1、蓝藻异形胞分化的分子机理。鉴别出在异形胞分化和图式形成起重要作用的基因丛hetZ-patU5-patU3，解析出HetZ和PatU3的作用机理；发现主调控因子HetR的识别序列、形态素小肽PatS的加工过程，以及hetR/patS与hetZ的相互调控关系。基于这些研究，提出以HetR-[HetZ/HetP]-PatS为核心的异形胞分化调控回路，为弄清异形胞分化和图式形成的分子机理作出了贡献。 

2、藻类在南极的适应机理和在温带的越冬机理。a) 分析比较相互分离约260万年的小球藻南极株和温带株，发现小球藻在南极环境的早期适应机制，即通过突变提高LEA蛋白和关键代谢步骤的酶在细胞内的含量，较快获得抗冻能力和在低温下的生长能力；b) 发现低温预处理能够大大强化中温蓝藻对于寒冷光照胁迫的耐受性(ACLT)，揭示出alpha-维生素E、RNA结合蛋白1和亚精胺等因子对于低温诱导蓝藻形成越冬力的重要作用，开启了蓝藻越冬的分子遗传学研究。 

3、藻类基因工程和合成生物学。研发出持续杀灭蚊蚴虫的基因工程鱼腥藻，获得可开放式培养产出gamma-亚麻酸的基因工程细鞘丝藻；开展了蓝藻基因组的简化和功能模块组装研究。

代表性论文：

1. Wei Zhang, Ye Du, Ivan Khudyakov, Qing Fan, Hong Gao, Degang Ning, C. Peter Wolk and Xudong Xu*, 2007. A gene cluster that regulates both heterocyst differentiation and pattern formation in Anabaena sp. strain PCC 7120. Molecular Microbiology, 66: 1429-1443. 

2. Ye Du, Yan Cai, Shengwei Hou and Xudong Xu*, 2012. Identification of the HetR-recognition sequence upstream of hetZ in Anabaena sp. Strain PCC 7120. Journal of Bacteriology, 194: 2297-2306. 

3. He Zhang, Shuai Wang, Yali Wang, Xudong Xu*, 2018. Functional overlap of hetP and hetZ in regulation of heterocyst differentiation in Anabaena sp. strain PCC 7120. Journal of Bacteriology, 200: e00707-17. 

4. Chao Li, He Zhang, Yaru Du, Wei Zhang, Xudong Xu*, 2021. Effects of PatU3 peptides on cell size and heterocyst frequency of Anabaena sp. PCC 7120. Journal of Bacteriology, 203: e00108-21.

5. Yang Yang, Chuntao Yin, Weizhi Li, Xudong Xu*, 2008. α-tocopherol is essential for the acquired chill-light tolerance (ACLT) in the cyanobacterium Synechocystis sp. PCC 6803, Journal of Bacteriology, 190: 1554-1560. 

6. Xiaoming Tan, Tao Zhu, Si Shen, Chuntao Yin, Hong Gao, Xudong Xu*, 2011. Role of Rbp1 in the acquired chill-light tolerance of cyanobacteria. Journal of Bacteriology, 193: 2675-2683. 

7. Xiangzhi Zhu, Qiong Li, Chuntao Yin, Xiantao Fang, Xudong Xu*, 2015. Role of spermidine in overwintering of cyanobacteria. Journal of Bacteriology, 197: 2325-2334.

8. Yali Wang, Xiaoxiang Liu, Hong Gao, Hong-Mei Zhang, An-Yuan Guo, Jian Xu, Xudong Xu*, 2020. Early stage adaptation of a mesophilic green alga to Antarctica: systematic increases in abundance of enzymes and LEA proteins. Molecular Biology and Evolution, 37: 849-863. 

专利：

1.一种利于收获的蓝藻的基因转移方法（ZL 00 1 28152.6）；

2.用于促进集胞藻分泌氨基酸的培养基、培养方法和藻株 （ZL 2017 1 0651573.4）

论著：

Xudong Xu, Jeff Elhai, C. Peter Wolk, 2008. Transcriptional and developmental responses by Anabaena to deprivation of fixed nitrogen. In The Cyanobacteria: Molecular Biology, Genomics and Evolution (Ed. T Herrero & E Flore), Horizon Scientific Press, Norwich, UK. p.383-422.