一、基本信息
杨世辉，博士，教授，博士生导师，省部共建生物催化与酶工程国家重点实验室副主任
电子邮件：shhyoung@hotmail.com
研究领域：微生物代谢工程，合成生物学，绿色生物制造
社会兼职：中国生物发酵产业协会第二届理事会理事，湖北省微生物学会及武汉微生物学会第十三届理事会工业微生物学专业委员会委员；PLoS ONE学术编辑（Academic Editor）；Energies编辑；Frontiers in Bioengineering and Biotechnology及Frontiers in Energy Research副编辑；Dataset Papers in Bioinformatics编委；《合成生物学》编委
实验室网页：http://bio.hubu.edu.cn/shihuiyang.htm
二、教育背景
2000.09–2005.05 美国加州大学河滨分校，理学博士
1997.09–2000.07 武汉大学生命科学学院，理学硕士
1989.09–1993.07 湖北大学生命科学系，理学学士
三、工作经历
2016至今 湖北大学生命科学学院，教授
2011.02–2016 美国能源部国家可再生能源实验室，Staff Scientist
2007.02–2011.0.2 美国能源部橡树岭国家实验室，Research Associate
2005.05–2007.02 美国威斯康星大学密尔沃基分校生物学系，博士后
1993.07–1997.06 湖北省襄樊市新药特药公司销售员及质检科科长
四、科研项目
1. 运动发酵单胞菌葡萄糖代谢产乳酸与乙醇碳分流机制的研究，国家自然科学基金，面上项目，2020.01–2023.12，主持
2. DNA修复系统影响运动发酵单胞菌辐射敏感性分子机制的研究，国家自然科学基金，联合基金项目，2020.01–2022.12，主持
3. 高版本模式微生物底盘细胞，科技部，国家重点研发计划“合成生物学”重点专项，2019–2023，子课题负责人
4. 2020年中国–中东欧合成生物学科研与人才培养合作项目，中国教育国际交流协会, 2020–2021，主持
5. 秸秆类资源生产生物能源产品关键技术研究，湖北省科技厅，湖北省技术创新专项（对外科技合作类），2019–2021，主持
五、发表论文
（一）（共同）第一或通讯作者论文（文章共>70篇；总引用2800, H–因子: 30），https://www.researchgate.net/profile/Shihui_YANG：
1. Yang Q, Yang Y, Tang Y, Wang X, Chen Y, Shen W, Zhan Y, Gao J, Wu B, He M, Chen S, Yang S^*. (2020) Development and characterization of acidic–pH tolerant mutants of Zymomonas mobilis through adaptation and next generation sequencing based genome resequencing and RNA–Seq. Biotechnology for Biofuels 13, 144.
2. Li R, Jin M, Du J, Li M, Chen S, Yang S^*. (2020) The magnesium concentration in yeast extracts is a major determinant affecting ethanol fermentation performance of Zymomonas mobilis. Frontiers in Bioengineering and Biotechnology. 8, 957.
3. Qiu M, Shen W, Yan X, He Q, Cai D, Chen S, Wei H, Knoshaug EP, Zhang, M, Himmel ME, Yang S*. (2020) Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production. Biotechnology for Biofuels 13,15.
4. Yang S*, Franden MA, Wang X, Chou YC, Hu Y, Brown SD, Pienkos PT, Zhang M*. (2020). Transcriptomic profiles of Zymomonas mobilis 8b to furfural acute and long-term stress in both glucose and xylose conditions. Frontiers in Microbiology 11, 13–13.
5. Hu L, Yang Y, Yan X, Zhang T, Xiang J, Gao Z, Chen Y, Yang S^*, Fei Q^*. (2020). Molecular mechanism associated with the impact of methane/oxygen gas supply ratios on cell growth of Methylomicrobium buryatense 5GB1 through RNA-Seq. Frontiers in Bioengineering and Biotechnology 8, 263.
6. Wang L, Chen L, Yang S^*, Tan X^*. (2020). Photosynthetic conversion of carbon dioxide to oleochemicals by cyanobacteria, recent advances and future perspectives. Frontiers in Microbiology
7. Yang Y, Rong Z, Song H, Yang X, Li M, Yang S^*. (2020) Identification and characterization of ethanol inducible promoters of Zymomonas mobilis based on omics data and dual reporter-gene system. Biotechnology and Applied Biochemistry
8. Zheng Y, Han J, Wang B, Hu X, Li R, Shen W, Ma X, Ma L, Yi L*, and Yang S*, Peng W*. (2019) Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system of Zymomonas mobilis for genome engineering. Nucleic Acids Research 47, 11461–11475.
9. Shen W, Zhang J, Geng B, Qiu M, Hu M, Yang Q, Bao W, Xiao Y, Zheng Y, Peng W, Zhang G, Ma L, Yang S*. (2019) Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis. Microbial Cell Factories 18,162.
10. Yang Y^#, Shen W^#, Huang J, Li R, Xiao Y, Wei H, Chou YC, Zhang M, Himmel ME, Chen S, Yi L, Ma L, Yang S^*. (2019). Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era. Biotechnology for Biofuels. 12,52.
11. Xia J, Yang Y, Liu C, Yang S^*, Bai F^*. (2019). Engineering Zymomonas mobilis for robust cellulosic ethanol production. Trends in Biotechnology. 37, 960–972.
12. Wei H^#*, Yang Y^#, Himmel ME, Tucker M.P, Ding S, Yang S^#, Arora R^*. (2019). Identification and characterization of five cold stress-related rhododendron dehydrin genes, spotlight on a FSK-type dehydrin with multiple F-segments. Frontiers in Bioengineering and Biotechnology. 7,30.
13. He Q^#, Yang Y^#, Yang S^#, Donohoe BS, Wychen S Van, Zhang M, Himmel ME, Knoshaug EP* (2018) Oleaginicity of the yeast strain Saccharomyces cerevisiae D5A Biotechnology for Biofuels 11,258
14. Yang S^#*, Vera J M^#, Savvakis G, Moskvin O V, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert A S, Coon JJ, Bates DM, Sato TK, Brown SD, Himmel ME, Zhang M, Landick R, Pappas KM*, Zhang Y^*. (2018) Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 Biotechnology for Biofuels 11,125
15. Wang X^#, He Q^#, Yang Y^#, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM*, Yang S*. (2018) Advances and prospects in metabolic engineering of Zymomonas mobilis. Metabolic Engineering 50, 57–73
16. Yang S*, Franden MA, Yang Q, Chou YC, Zhang M, Pienkos PT* (2018) Identification of inhibitors in lignocellulosic slurries and determination of their effect on hydrocarbon-producing microorganisms. Frontiers in Bioengineering and Biotechnology 6,23
17. Yang Y, Hu M, Tang Y, Geng B, Qiu M, He Q, Chen S, Wang X*, Yang S*. (2018) Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis. Bioresources and Bioprocessing 5, 6.
18. Yang S^#*, Fei Q^#, Zhang Y, Contreras, L M, Utturkar, S M, Brown, S D, Himmel ME, Zhang M* (2016) Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microbial Biotechnology 9, 699–717.
19. Yang S*, Mohagheghi A, Chou YC, Franden MA, Chen XW, Dowe N, Himmel M, Zhang M. * (2016) Metabolic engineering of Zymomonas mobilis for production of 2,3-butanediol from lignocellulosic biomass sugars Biotechnology for Biofuels 9,189
20. Yang S*, Franden A, Chou YC, Brown SD, Pienkos PT, Zhang M*. (2014) Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates. Biotechnology for Biofuels 7,140.
21. Yang S*, Pan C, Hurst GB, Dice, L, Davison BH, Brown SD*. (2014) Elucidation of Zymomonas mobilis physiology and stress responses to acetate by quantitative proteomics and transcriptomics Front Microbiol 5, 246.
22. Yang S, Pan C, Tschaplinski TJ, Hurst GB, Engle NL, Zhou W, Dam P, Xu Y, Rodriguez, MJr, Dice L, Johnson CM, Davison BH, Brown SD. (2013) Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses PLoS ONE 8, e68886.
23. Yang S, Land, ML, Klingeman, DM, Pelletier DA, Lu ST, Martin SL, Guo HB, Smith JC, Brown SD. (2010) Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 107, 10395–10400.
24. Yang S, Pelletier D A, Lu ST, Brown SD. ( 2010) The Zymomonas mobilis regulator Hfq and related Saccharomyces cerevisiae proteins contribute to tolerance against multiple lignocellulosic pretreatment inhibitors BMC Microbiology 10, 135
25. Yang S, Pappas KM, Hauser LJ, Chen GL, Hurst GB et al. (2009) Improved genome annotation for Zymomonas mobilis. Nature Biotechnology 27, 893–894. (IF 29.49)
26. Yang S^#, Tschaplinski, TJ, Engle, NL, Carroll SL, Martin SL, Davison BH, 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)
27. Wang W^#*, Yang S^#*, Pienkos PT, Johnson D. (2014) Connecting lignin-degradation pathway with pretreatment inhibitor sensitivity of Cupriavidus necator. Front Microbiol 5, 247.
28. Yang S*, Guarnieri MT, Smolinski, S, Ghirardi, M, Pienkos, PT. (2013) De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq Biotechnology for Biofuels 6,118.
29. Wilson, C M^#*, Yang S^#, Rodriguez MJr, Ma Q, Johnson CM, Dice L, Xu Y, Brown SD. (2013) Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. Biotechnology for Biofuels 6,131.
30. Yang S, Giannone R J, Dice L, Yang Z K, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD. (2012) Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 13, 336.
31. 杨永富#， 耿碧男#，宋皓月，何桥宁，何明雄，鲍杰，白凤武*，杨世辉* 运动发酵单胞菌底盘细胞研究现状及展望合成生物学 http://wwwsynbiojcom/CN/abstract/abstract111shtml
（二）书籍章节
1. Yang Y, Qiu M, Yang Q, Wang Y, Wei H, Yang S*. (2020) Connecting Microbial Genotype with Phenotype in the Omics Era In: Himmel M, Bomble Y (eds) Metabolic Pathway Engineering Methods in Molecular Biology, 2096: 217–233 https://doiorg/101007/978-1-0716-0195-2_16 Humana, New York, NY
2. Bai FW Yang S, Ho N. (2019) Fuel ethanol production from lignocellulosic biomass P49–65 In: Comprehensive Biotechnology, Edition 3, Edited by Murray Moo–Young Elsevier BV, Netherlands
3. Yang S, Wang W, Wei H, Himmel M, Zhang, M. (2015) Identification of genetic targets to improve lignocellulosic hydrocarbon production in Trichoderma reesei using public genomic and transcriptomic datasets P177–196 In Direct Microbial Conversion of Biomass to Advanced Biofuels Edited by Michael E Himmel Elsevier New York, US
4. Yang S, Klingeman, DM, Brown SD. (2012) Ethanol-tolerant gene identification in Clostridium thermocellum using pyro-resequencing for metabolic engineering P111–136 In Methods in Molecular Biology: Microbial Metabolic Engineering Edited by Cheng Q Human Press New York, US
5. Yang S, Klingeman D M, Brown SD. (2011) Genomics on pretreatment inhibitor tolerance of Zymomonas mobilis P161–176 In: Microbial stress tolerance: from genomics to biofuels Microbiology monographs (Springer series) Edited by Liu Z L Springer Heidelberg, Germany
6. Yang CH, Yang S. (2008) Managing bacterial plant diseases by modulating quorum sensing and Type III secretory systems P16–57 In: Biotechnology and Plant Disease Management Eds Punja ZK, De Boer SH, and Sanfacon H CABI Publishing Oxfordshire UK
六、代表专利
1. Yang S, Linger J, Franden A, Pienkos PT, Zhang M. US** Biocatalysts with enhanced inhibitor tolerance.
2. Brown. S, Yang, S. US Microorganisms having enhanced resistance to acetate and related compositions and methods of Use .
3. Brown S, Guss A, Yang S, Karpinets T, Lynd, L. US Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol.
4. Brown S, Yang S. US Microorganisms having enhanced tolerance to inhibitors and stress.
5. Yang CH, Yang S. US and WIPO WO/2008/124836 Methods of reducing virulence in bacteria.
6. 杨世辉，杨青CNA 一株耐受低pH的乙醇生产运动发酵单胞菌菌株及其分离筛选方法和应用 2018年9月19日，发明专利申请
7. 杨世辉，杨永富，沈威，李闰霞，黄钜，王禺，易犁，马立新 PCT/CN2019/086173 一种基于双荧光报告基因系统鉴定生物元件的方法及基于该方法构建的生物元件库 2019年5月9日，发明专利申请
8. 杨世辉，彭文舫，沈威，郑艳丽，易犁，马立新 PCT/CN2019/112556一种基于运动发酵单胞菌的CRISPR-Cas系统、基因组编辑体系及其应用 2019年7月30日, 发明专利申请
七、荣誉和奖励
1. 湖北大学优秀教师（2018–2020年度，2016–2018年度）
2. 美国国家可再生能源实验室月度员工奖、项目贡献奖（2015）
3. 美国橡树岭国家实验室生物科学部研究助理卓越成就奖（2009.11，1年1个）
4. 美国加州大学河滨分校GSA Minigrant（2003，2004）
5. 美国加州大学河滨分校克劳资纪念奖（2003）
6. 第三届ASM & TIGR微生物基因组会议旅行奖（2003）
7. 美国加州大学河滨分校詹姆斯和艾德琳华莱士年度奖（2002，1年1个）
8. 加州大学河滨分校校长卓越奖学金（2000–2005）
9. 湖北大学iGEM团队（2次银奖），主要指导教师（2018、2019）