发布时间:2016-09-26    点击率:

姓  名: 杨世辉
办公电话: 15607121038(手机);传真:027-86747980
电子邮件: shhyoung@hotmail.com 
通讯地址: 湖北省武汉市武昌区友谊大道368号湖北大学生命科学学院
主要研究领域:分子微生物学,代谢工程,功能基因组学和生物信息学, 合成生物学,系统生物学,生物能源、生物防治及微生物-宿主相互作用
主要社会兼职:PLoS ONE 学术编辑(Academic Editor); Energies 编辑; Nature Frontiers in Microbiology 副编辑及主题编辑; Dataset Papers in Bioinformatics 编委
Science, PNAS, PLoS Genetics, Molecular and Cellular Proteomics, Bioinformatics, PLoS One, Bioresource Technology, Biotechnology for Biofuels, BMC Genomics等学术杂志审稿人
多次应邀在各种国际学术会议上做大会报告(ACS Annual Meeting; Society for Industrial Microbiology & Biotechnology (SIMB) Annual Meeting; Symposium on Biotechnology for Fuels and Chemicals)并作为会议分会主持人(35th-38th SIMB Symposium on Biotechnology for Fuels and Chemicals)
2007年2月-2011年2月,美国能源部橡树岭国家实验室,副研究员(Research Associate)
2011年2月-2016年,美国能源部国家可再生能源实验室,研究员(Staff Scientist)
1. 湖北省生物资源绿色转化协同创新中心启动经费(湖北省科技厅),400万,2016-2021,主持
2. NREL LDRD. Small RNA and Riboswitches: A New Frontier for Biofuels Strain Engineering. 2015-2017. Eric Knoshaug (PI), Shihui Yang (Co-PI), and Bryon Donohoe (Co-PI). 
3. NREL LDRD Seed Project. 2015. Integrated Approach to Connect Genetic Profiles with Microstructural Phenotypes Involved in Biofuel Production in Green Algae. Alexandra Dubini (PI), Shihui Yang (Co-PI), and Peter Ciesielski (Co-PI). 
4. DOE Office of Science, Systems Biology of Bioenergy-Relevant Microbes to Enable Production of Next-Generation Biofuels. 2014. Unravel lipid accumulation mechanism in oleaginous yeast through single-cell systems biology study. Sunney Xie (PI), Shi-You Ding (Co-PI). Shihui Yang (Key personnel on single-cell transcriptomic data analysis and metabolic engineering). 
5. NREL License Revenue-Funded Project. 2013-2014. Genetic elements and microorganisms conferring enhanced tolerance to pretreated corn stover hydrolysate. Shihui Yang (PI).
代表性论文(通讯作者#与共同第一作者*文章: 24,共40篇;总引用>1000, H-因子: 18):
Ethanologenic Zymomonas mobilis: 
1. Yang, S. *#, Fei., Q.*, Zhang, Y., Contreras, L. M., Utturkar, S. M., Brown, S. D., Himmel, M.E., and Zhang, M#. 2016. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microbial Biotechnology (In Press). 
2. Yang, S.#, Mohagheghi, A., Franden, A., Chou, Y-C., Dowe, N., Himmel, M. E., and Zhang, M#. 2016. Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars. Biotechnol Biofuels 9:189. 
3. Yang, S.#, Franden, A., Chou, Y-C., Brown, S. D., Pienkos, P. T., and Zhang, M#. 2014. Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates. Biotechnol Biofuels 7:140. 
4. Yang, S.#, Pan, C., Hurst, G. B., Dice, L., Davison, B. H., and Brown, S. D.#. 2014. Elucidation of Zymomonas mobilis physiology and stress responses to acetate by quantitative proteomics and transcriptomics. Front. Microbiol. 5:246. doi: 10.3389/fmicb.2014.00246. 
5. Yang, S., Pan, C., Tschaplinski, T. J., Hurst, G.B. Engle, N. L., Zhou, W., Dam, P., Xu, Y., Rodriguez, M. Jr., Dice, L., Johnson, C. M., Davison, B. H., and Brown, S. D. 2013. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. PLoS ONE 8(7): e68886. 
6. Yang, S., Land, M. L., Klingeman, D. M., Pelletier, D. A., Lu, S. T., Martin, S. L., Guo, H. B., Smith, J. C., and Brown, S. D. 2010. Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 107: 10395–10400. 
Faculty of 1000 recommended: http://ec2-176-34-150-24.eu-west-1.compute.amazonaws.com/prime/10030959
7. Yang, S., Pelletier, D. A., Lu, S. T, and Brown, S. D. 2010. The Zymomonas mobilis regulator Hfq and related Saccharomyces cerevisiae proteins contribute to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiol. 10: 135. 
8. Yang, S., Pappas, K. M., Hauser, L. J., Land, M. L., Chen, G-L, Hurst, G.B. et al. 2009. Improved genome annotation for Zymomonas mobilis. Nat. Biotechnol. 27: 893 –4. 
9. Yang, S., Tschaplinski, T. J., Engle, N. L., Carroll, S. L., Martin, S. L., Davison, B. H., Palumbo, A. V., Rodriguez, M. Jr., and Brown, D., S. 2009. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentation. BMC Genomics 10: 34. (Highly accessed).
Thermophilic Clostridium thermocellum:
10. Xu, Q., Resch, M., Podkaminer, K., Yang, S., Baker, J., Donohoe, B., Wilson, C., Klingeman, D. M., Olson, D., Decker, S., Giannone, R. J., Hettich, R. L., Brown, S. D., Lynd, L. R., Bayer, E. A., Himmel, M. E., and Bomble, Y. 2016. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. Science Advances. 2(2): e1501254.
11. Wilson, C. M.*, Yang, S.*, Rodriguez, M. Jr., Ma, Q. , Johnson, C. M., Dice, L., Xu, Y., and Brown, S. D. 2013. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. Biotechnol Biofuels 6:131. 
12. Yang, S., Giannone, R. J., Dice, L., Yang, Z. K., Engle, N. L., Tschaplinski, T. J., Hettich, R. L., and Brown, S. D. 2012. Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 13:336. 
13. Brown, S. D., Guss, A. M., Karpinets, T. V., Parks, J. M., Smolin, N., Yang, S., Land, M. L., et al. 2011. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc. Natl. Acad. Sci. USA. 108: 13752-7. 
14. Wei, H., Fu, Y., Magnusson, L., Baker, JO., Maness, PC., Xu, Q., Yang, S., Bowersox, A., Bogorad, I., Wang, W., Tucker, MP., Himmel, ME., Ding, S. 2014. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front. Microbiol. 5:142.
Molecular Microbe-Plant Interactions:
15. Yang, S., Peng, Q., Zhang, Q., Zou, L., Li, Y., Robert, C. et al. 2010. Genome-wide identification of HrpL-regulated genes in necrotrophic phytopathogen Dickeya dadantii 3937. PLoS ONE 5(10): e13472. 
16. Yang, S.*, Peng, Q.*, San Francisco, M., Wang, Y., Zeng, Q., and Yang, C.-H. 2008. Type III secretion system genes of Dickeya dadantii 3937 are induced by plant phenolic acids. PLoS ONE 3(8): e2973. 
17. Yang, S., Zhang, Q., Peng, Q., Yi, X., Chang, J. C., Reedy, R. M., Charkowski, A. O., and Yang, C.-H. 2008. Dynamic regulation of GacA in type III secretion system, pectinase gene expression, pellicle formation, and pathogenicity of Dickeya dadantii. Mol. Plant-Microbe Interact. 21: 133-142. 
18. Yang, S., Zhang, Q., Guo, J., Charkowski, A. O., Glick, B. R., Ibekwe, A. M., Cooksey, D. A., and Yang, C.-H. 2007. Global effect of indole-3-acetic acid (IAA) biosynthesis on multiple virulence factors of Erwinia chrysanthemi 3937. Appl. Env. Microbiol. 73:1079-1088. 
19. Peng, Q.*, Yang, S.*, Charkowski, A. O., Yap, M. N., Steeber, D. A., Keen, N. T., and Yang, C.-H. 2006. Population behavior analysis of dspE and pelD expression in Erwinia chrysanthemi 3937. Mol. Plant-Microbe Interact. 19: 451-7. 
20. Yang, S., Perna, N. T., Cooksey, D. A., Okinaka, Y., Lindow, S. E., Ibekwe, A. M., Keen, N. T., and Yang, C-H. 2004. Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol. Plant-Microbe Interact. 17: 999-1008. 
Others (Lignin, Systems biology, Meta-transcriptomics, and Bioinformatics etc.): 
21. Yang, S # Wang, W.#, Wei, H., Wychen, S. V., Pienkos, P. T., Zhang, M., and Himmel, M. 2016. Impact of nitrogen deficiency strategies on lipid production for yeast and fungal species. Energies. 9:685.
22. Wang, W*#., Yang, S.*#, Pienkos, P. T., and Johnson, D. 2014. Connecting lignin-degradation pathway with pretreatment inhibitor sensitivity of Cupriavidus necator. Front. Microbiol. 5:247. 
23. Zeng, Y., Zhao, S., Yang, S., and Ding, S. 2014. Lignin plays the negative role in the biochemical process for producing lignocellulosic biofuels. Curr. Opin. Biotechnol. 27: 38-45. 
24. Yang, S.#, Guarnieri, M. T., Smolinski, S., Ghirardi, M., and Pienkos, P. T. 2013. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. Biotechnol Biofuels 6:118. 
25. Chou, W-C., Ma, Q., Yang, S., Cao, S., Brown, S. D., and Xu, Y. 2015. Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Res. doi: 10.1093/nar/gkv177.  
26. Guarnieri, M. T., Nag, A., Yang, S., and Pienkos, P. T. 2013. Proteomic analysis of Chlorella vulgaris: Potential targets for enhanced lipid accumulation. J Proteomics. pii: S1874-3919(13)00278-9.  
1. Yang, S., Linger, J., Franden, A., Pienkos, P. T., and Zhang, M. US14265039. Biocatalysts with enhanced inhibitor tolerance.
2. Brown, S., and Yang, S. US20130078691. Microorganisms having enhanced resistance to acetate and related compositions and methods of Use. 
3. Brown, S., Guss, A., Yang, S., Karpinets, T., and Lynd, L. US20110287499. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol.
4. Brown, S., and Yang, S. US20100311137. Microorganisms having enhanced tolerance to inhibitors and stress.
5. Yang, C.-H., and Yang, S. US20100249234 and WIPO WO/2008/124836. Methods of reducing virulence in bacteria. 
1. 2015年12月 美国国家可再生能源实验室项目贡献奖
2. 2015年4月 美国国家可再生能源实验室月度员工奖
3. 2009年11月 橡树岭国家实验室生物科学部研究助理卓越成就奖(1年1个)
4. 2003年                 加州大学河滨分校克劳资纪念奖
5. 2002年       加州大学河滨分校詹姆斯和艾德琳华莱士年度奖(1年1个) 
6. 2000年-2005年       加州大学河滨分校校长卓越奖学金



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