1）新型微生物酶制剂基因筛选及应用

利用未培养元基因组以及单细胞未培养微生物技术，通过高通量酶分子筛选技术收集各种特殊环境（包括热泉、盐湖、大洋、冰川等）极端微生物酶新基因资源，通过基因高效表达工程菌构建，开拓酶制剂在工业、农业、环保、健康、能源等领域的应用价值；

2）酶分子定向进化

采用分子定向进化等技术对酶制剂进行分子改造，探索酶分子结构与功能相互关系，获得更高效率、更好稳定性和使用性的新型酶分子。

3）丝状真菌高效表达系统研究

探索木霉、黑曲等丝状真菌高效分泌表达系统调控机制，研发新型丝状真菌高效微生物分泌表达系统，构建酶制剂高效表达基因工程菌。

近期代表性论文（* 通讯作者）

1、Improving heterologous gene expression in Aspergillus niger by introducing multiple copies of protein-binding sequence containing CCAAT to the promoter    Letters in Applied Microbiology 2003,36,358-361  

2、The synergetic effefts of two CCAAT boxes in Aspergillus niger glaA gene promoter on activation of PglaA transcription  Science in China, Ser. C Vol 47 No 2 139~147 2004   

3、耐碱性木聚糖酶基因在短小芽孢杆菌中高效分泌表达研究  微生物学报 2004，44（4）1

4、黑曲霉糖化酶和木聚糖酶基因在工业酿酒酵母中的共表达 菌物系统  2004，23（4）：494～501

5、黑曲霉木聚糖酶在工业酒精酵母中的分泌表达 微生物学报 2005，45（1）135－138

6、Prokaryotes Diversity in the Rumen of Yak (Bos grunniens) and Jinnan Cattle  (Bos taurus) estimated by 16S rDNA homology analyses.  Anaerobe 11  207-215, 2005

7、Isolation and identification of one bacterial strain from a 3900 meter deep subsurface rocks Acta Pertrologica Sinica 2005 21(2) 540-544  

8、Analysis of Bacterial Community in Donghai Terrestrial Deep Subsurface  Acta Pertrologica Sinica 200521(2) 533-539    

9、云南腾冲热泉土壤微生物基因组文库的构建与分析  微生物学报 2006 46（3）427－431

10、Wang YL, Xia Y, Dong XZ, Dong HL, Yang KQ, Dong ZY, Huang L. Quantitative analysis of two uncultured bacterial species from the terrestrial deep subsurface  by real-time PCR. Acta Pertrologica Sinica 2006, 22(9): 2103-2106.

11、 Wang YL, Guangyu Li,Yang KQ, Huang L and Dong Zhiyang. Molecular methods in microbiology study of rock-Microbial research in Chinese continental. Acta Pertrologica Sinica 2006, 22(9): 2107-2111. 

12、荷斯坦奶牛瘤胃微生物元基因组BAC文库的构建与分析  微生物学报 2007 47（2）：213～216

13、Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring    

Applied  Microbiology and Biotechnology 2007 75：367－376

14、Multistate folding of a hyperthermostable Fe-superoxide dismutase (TcSOD)

in guanidinium hydrochloride: The importance of the quaternary structure

Biochimica et Biophysica Acta 1784 (2008) 445–454

15、Wang YL, Xia Y, Dong XZ, Dong HL, Yang KQ, Dong ZY Isolation and identification of one bacterial strain from a 3900 meter deep subsurface rocks Acta Pertrologica Sinica 2005 21(2) 540-544  

16、Wang YL, Guangyu Li,Yang KQ, Huang L and Dong Zhiyang Analysis of Bacterial Community in Donghai Terrestrial Deep Subsurface  Acta Pertrologica Sinica 2005 21(2) 533-539

17、 Wang YL, Xia Y, Dong XZ, Dong HL, Yang KQ, Dong ZY, Huang L. Quantitative analysis of two uncultured bacterial species from the terrestrial deep subsurface  by real-time PCR. Acta Pertrologica Sinica 2006, 22(9): 2103-2106.

18、 Wang YL, Guangyu Li,Yang KQ, Huang L and Dong Zhiyang. Molecular methods in microbiology study of rock-Microbial research in Chinese continental. Acta Pertrologica Sinica 2006, 22(9): 2107-2111.

19、 Yong-Zhi He, Ke-Qiang Fan, Cui-Juan Jia, Zhi-Jun Wang, Wu-Bin Pan, Li Huang, Ke-Qian Yang, Zhi-Yang Dong. Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring. Applied Microbiology and Biotechnology 2007, 75: 367-376.

20、Yong-Zhi He, Ke-Qiang Fan, Cui-Juan Jia, Zhi-Jun Wang, Wu-Bin Pan, Li Huang, Ke-Qian Yang, Zhi-Yang Dong，（2007）Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring. Applied Microbiology and Biotechnology 75: 367-376

21. Sha Wang, Wei-Feng Liu, Yong-Zhi He , Ao Zhang , Li Huang , Zhi-Yang Dong,Yong-Bi Yan,(2008)  Multistate folding of a hyperthermostable Fe-superoxide dismutase (TcSOD)in guanidinium hydrochloride: The importance of the quaternary structure. Biochimica et Biophysica Acta 1784: 445–454.

22、Xiaoyun Su, Xin Chu, Zhiyang Dong.(2009) Identification of elevated transcripts in a Trichoderma reesei strain expressing a chimeric transcription activator using suppression subtractive hybridization. World J Microbiol Biotechnol  25:1075–10845

23、Xiaoyun Su , Shan Zhang, Li Wang , Zhiyang Dong (2009)Overexpression of IbpB enhances production of soluble active Streptomyces olivaceovirdis XynB in Escherichia coli Biochemical and Biophysical Research Communications 390  673–677

24、Li Wang, Zhong-jun Hu, Yuan-ming Luo, Yan-wu Huo, Qing Ma, Yong-zhi He, Yu-ying Zhang,Fei Sun, Zhi-yang Dong（2010）Distinct symmetry and limited peptide refolding activity of  the thermosomes from the acidothermophilic archaea Acidianus tengchongensis S5T  Biochemical and Biophysical Research Communications  2010 (393) pp. 228-2

25、Shan Zhang, Kai Zhangb, Xiuzhen Chena, Xin Chua, Fei Sunb and Zhiyang Dong  Five mutations in N-terminus confer thermostability on mesophilic ylanase   Biochemical and Biophysical Research Communications 395 (2010)200-206

26、Yanwu Huo＃, Z. H. ＃, Kai Zhang＃, Li Wang, Yujia Zhai, Qiangjun Zhou, Gabe Lander, Jiang Zhu, Yongzhi He, Xiaoyun Pang, Wei Xu, Mark Bartlam, Zhiyang Dong, Fei Sun Crystal  Structure of Group II Chaperonin in the OpenState. Structure 2010 18 (10)

申请或授权专利

1、木聚糖酶及其生产方法与生产专用菌株（02131439.X）

2、一种木聚糖酶及其生产方法与生产专用菌株（2003101032463）

3、一种耐热超氧化物歧化酶及其编码基因与应用（zl200510005207.9

4、一种转录激活因子及其编码基因与应用（200710177828.4）

5、“TrMAK蛋白在调节纤维素酶产量中的应用”申请号：201210247669.1

6、“TrPK蛋白在调节纤维素酶产量中的应用”申请号：201210247397.2

7、 “来源于里氏木霉的一个蛋白质及其基因的用途”？申请号：？201210264070.9？

8、“高通量筛选高效表达外源蛋白的重组里氏木霉的方法”申请号：201210271826.2