从资源发掘、机制研究到应用开发，系统进行极端微生物这一重要遗传资源的认识、保护、开发和持续利用，主要包括:极端环境的微生物区系生态与生物多样性，极端微生物生理机制及分子基础，极端微生物功能与产物的生物技术利用和合成生物制造。

1.Zhou H, Zhang Y, Long CP, Xia X, Xue Y, Ma Y, Antoniewicz MR, Tao Y, Lin B. (2024) A citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations. Nat Commun. 15(1):2372. doi: 10.1038/s41467-024-46655-4.

2.Liu C, Yue Y, Xue Y, Zhou C, Ma Y. (2023) CRISPR-Cas9 assisted non-homologous end joining genome editing system of Halomonas bluephagenesis for large DNA fragment deletion. Microb Cell Fact. 22(1):211. doi: 10.1186/s12934-023-02214-y.

3.Ma X, Jiang K, Zhou C, Xue Y, Ma Y. (2022) Identification and characterization of a novel GNAT superfamily Nα -acetyltransferase from Salinicoccus halodurans H3B36. Microb Biotechnol. 15(5):1652-1665. doi: 10.1111/1751-7915.13998.

4.Zhou C, Cao Y, Xue Y, Liu W, Ju J, Ma Y. (2022) Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming. Int J Mol Sci. 24(1):538. doi: 10.3390/ijms24010538.

5.Bo Liu, Shuman Xiang, Guang Zhao, Bojun Wang, Yanhe Ma *, Weifeng Liu *, Yong Tao. (2019) Efficient production of 3-hydroxypropionate from fatty acids feedstock in Escherichia coli. Metabolic Engineering. 51:121-130.

6.Cheng Zhou, Hongliang Qin, Xiujuan Chen, Yan Zhang, Yanfen Xue, Yanhe Ma *. (2018)  A novel alkaline protease from alkaliphilic Idiomarina sp. C9-1 with potential application for eco-friendly enzymatic dehairing in the leather industry. Scientific Reports. 8(1):16467.

7.Cheng Zhou, Yanfen Xue, Yanhe Ma*. (2018)  Characterization and high-efficiency secreted expression in Bacillus subtilis of a thermo-alkaline β-mannanase from an alkaliphilic Bacillus clausii strain S10. Microbial Cell Factories.  17(1):124.

8.Deyong Ge, Yanfen Xue, Yanhe Ma*. (2016) Two unexpected promiscuous activities of the iron–sulfur protein IspH in production of isoprene and isoamylene. Microbial Cell Factories. 15:79.

9.Nilnate Assavasirijinda, Deyong Ge, Bo Yu, Yanfen Xue, Yanhe Ma*. (2016) Efficient fermentative production of polymer-grade d-lactate by an engineered alkaliphilic Bacillus sp. strain under non-sterile conditions. Microbial Cell Factories. 15:3.

10.Kai Jiang, Yanfen Xue, Yanhe Ma*. (2015) Identification of N(α)-acetyl-α-lysine as a probable thermolyte and its accumulation mechanism in Salinicoccus halodurans H3B36. Scientific Reports. 5: 18518

11.《Halophiles and hypersaline environments: current research and future trends》,Springer，Berlin，2011

12.《生物炼制-工业过程与产品》（上卷）译著, 化学工业出版社，2007

13.《高级酶工程》马延和主编，科学出版社，2022

国家973计划项目"生物炼制细胞工厂的科学基础"（2007-2012）;

国家973计划重大科学问题导向项目“人工合成细胞工厂” （2011-2015）;

国家863计划项目"极端微生物功能基因的克隆、表达与应用研究" (2001-2004);

国家科技重大专项"嗜盐碱微生物抗盐碱基因的克隆与功能验证"（2009-2010）;

中科院知识创新重大项目"纤维素乙醇的高温发酵与生物炼制"（2008-2011）;

创新团队国际合作伙伴计划课题“新型木质纤维素降解酶系的发现、改造与应用”2010-2012）;

欧盟第五框架计划项目"工业生物催化剂的多基因筛选技术"（2002-2004）