此页面上的内容需要较新版本的 Adobe Flash Player。

获取 Adobe Flash Player

姓  名: 杨云锋
所在单位: 生态学教研所
职  称: 正高级
邮寄地址: 清华大学环境学院
办公电话: 010- 62784692
电子邮件: yangyf@tsinghua.edu.cn
办公地点: 环境节能楼925室

教育背景

1996. 8 – 2003. 1 美国Albert Einstein College of Medicine生物专业,博士

2000. 1 – 2002. 5 美国City University of New York计算机专业,硕士 (第二学位)

1991. 9 – 1996. 7 中国科大生物系,学士

工作履历

2011.01-现在 清华大学环境学院,教授

2010.09-2011.01  清华大学环境科学与工程系,教授

2006.03-2010.09  美国橡树岭国家实验室生命科学部,研究员(staff scientist)

2006.08-2009.12  美国DENISON 大学,兼职教授(part-time professor)

2003.02-2006.03  美国橡树岭国家实验室环境科学部,博士后

教学:

研究生课程:现代环境生物监测原理与技术(2014-今)

研究生课程:高级微生物学 (2013-今)

本科课程Course BIOL325: Genetics (2007-2009)

本科课程Course BIOL201: Cell and Molecular Biology (2006)

 

学术兼职

BMC Microbiology杂志副主编(2014-今)

Applied and Environmental Microbiology 杂志编委(2013-今)

美国能源部 SBIR/STTR 项目评审(2007-2010)

International Journal of Functional Informatics and Personalised Medicine 杂志编委(2007-2009)

研究领域

利用宏基因组学技术解析微生物介导的地球化学循环的微观机理。针对我国节能减排、污染治理等环境领域的重大需求,研究环境变化如何影响微生物群落的功能基因,以及功能基因如何介导生物地球化学循环等科学问题。成果应用于评估环境变化对基因多样性的影响,利用微生物勘探油气、可燃冰矿藏,碳汇模型优化,微生物资源开发和基因工程等多个方向。

研究概况

近年主持或者参与主持的科研项目:

1. 城市污水高含固污泥高效厌氧消化装备开发与工程示范子课题(住建部水专项,2013-2016)

2. 碳循环关键过程及其与气候系统耦合的研究子课题(科技部973项目,2013-2017)

3. 冻土带天然气水合物微生物勘查技术子课题(科技部863项目,2012-2015)

4. 环境多因子对温带草原土壤微生物群落结构的影响(国家基金委面上项目,2012-2015)

5. 基于宏基因组学技术的工程系统微生物群落特征研究(国家重点实验室自主项目,2011-2013)

6.能源部生物能源中心梭菌遗传工程项目(美国能源部GTL项目, 2007 – 2012)

7. 杨树–微生物相互作用项目,分离微生物和遗传工程开发子课题(美国能源部GTL项目2009 – 2012)

8. 土壤微生物分布、转移过程中细胞胶结的定量分析子课题 (美国能源部ERSP exploratory项目2010 – 2011)

9.对重金属污染的地下水中分离和筛选功能微生物项目,分离微生物子课题(美国能源部ERSP项目,2007 – 2010)

10. 系统生物学方法理解植物抗旱性机理项目,功能基因组学分析和生物网络构建子课题(美国橡树岭国家实验室LDRD项目,2007 – 2010)

11. 合成气-醇类转换细菌的遗传工程开发(美国橡树岭国家实验室LDRD项目,2007 – 2010)

12. 食品生产过程中检测沙门氏菌的新型技术(Mars, Inc. 资助项目和美国橡树岭国家实验室Seed money项目2009 – 2010)

13. Shewanella Federation 还原金属分子机制子课题(美国能源部GTL项目,2006 – 2008)

14. 生物能源梭菌的遗传工程开发(美国橡树岭国家实验室Seed money项目, 2006 – 2007)

 

奖励与荣誉

1.清华大学环境学院科研先进个人(2013)

2. 清华大学"学术新人奖" (2014)

学术成果

发表文章

近五年论文引用次数800余次。

1. M. Zhao, K. Xue, F. Wang, S. Liu, S. Bai, B. Sun, J. Zhou and Y. Yang* (2014), Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping, The ISME Journal, doi: 10.1038/ismej.2014.46

2. S Liu, F Wang, K Xue, B Sun, Y Zhang, Z He, JD Van Nostrand, J Zhou, Y Yang* (2014), The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry, Environmental Microbiology, doi:10.1111/1462-2920.12398

3. H Chu, S Wang, H Yue, Q Lin, Y Hu, X Li, J Zhou, Y Yang* (2014), Contrasting soil microbial community functional structures in two major landscapes of the Tibetan alpine meadow, MicrobiologyOpen, accepted

4. Y Gao, S Wang, D Xu, H Yu, L Wu, Q Lin, Y Hu, X Li, Z He, Y Deng, J Zhou, Y Yang* (2014), GeoChip as a Metagenomics Tool to Analyze the Microbial Gene Diversity along an Elevation Gradient, Genomics Data, accepted

5. M Zhao, F Wang, Shanshan Liu, K Xue, Y Liang, S Bai, Z He, JDV Nostrand, J Zhou, Y Yang*, B Sun* (2014), GeoChip profiling of microbial community in response to global changes simulated by soil transplant and cropping, Genomics Data, accepted

6. Y. Sun, Y. Shen, P. Liang, J. Zhou, Y. Yang*, Xia Huang* (2014), The remarkable linkages between microbial functional potentials and wastewater constituents in large-scale operational membrane bioreactors for the municipal wastewater treatment, Water research 56, 162-171

7. Y Yang*, Y Gao, S Wang, D Xu, H Yu, L Wu, Q Lin, Y Hu, X Li, Z He, Y Deng, J Zhou (2014), The microbial gene diversity along an elevation gradient of the Tibetan grassland, The ISME Journal 8 (2), 430-440

8. J. Zhou, Y. Deng, P. Zhang, K. Xue, Y. Liang, JDV Nostrand, Y. Yang, Z. He, L. Wu, D. Stahl, T. Hazen, J. Tiedje, A. Arkin (2014), Stochasticity, succession, and environmental perturbations in a fluidic ecosystem, Proceedings of the National Academy of Sciences 111 (9), E836-E845

9. X Wang, Y Xia, X Wen, Y Yang, J Zhou (2014), Microbial Community Functional Structures in Wastewater Treatment Plants as Characterized by GeoChip, PLoS One 9(3): e93422

10. Y Zhang, J Cong, H Lu, C Yang, Y Yang, J Zhou, D Li (2014), An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types, PLoS One 9(4): e93773

11. Y Li, T Xu, T Tschaplinski, N Engle, Y Yang, D Graham, Z He, J Zhou (2014), Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation, Biotechnology for Biofuels 7 (1), 25

12. Y Xia, X Wang, X Wen, K Ding, J Zhou, Y Yang, Y Zhang (2014), Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors, Appl. Microbiol. Biotechnol, accepted.

13. Y Yang*, J Chen, D Qiu, J Zhou (2013), Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction, BMC microbiology 13 (1), 267

14. X Sun, Y Gao and Y Yang* (2013), Recent advancement in microbial environmental research using metagenomics tools,Biodiversity Science, 21 (4): 393–400

15. Y Yang* (2013), Omics breakthroughs for environmental microbiology, Microbiology China 40 (1), 18-33

16. Y Yang*, L. Wu, Q. Lin, M. Yuan, D. Xu, H. Yu, Y. Hu, J. Duan, X. Li, Z. He, K. Xue, J. Nostrand, S. Wang and J. Zhou (2013), Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland, Global Change Biology 19(2), 637–648

17. D Qiu, H Wei, Q Tu, Y Yang, M Xie, J Chen, MH Pinkerton, Y Liang, Z He, J Zhou (2013) Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1, Applied and environmental microbiology 79 (17), 5250-5257

18. G Mohr, W Hong, J Zhang, G Cui, Y Yang, Q Cui, Y Liu and AM Lambowitz (2013), A Targetron System for Gene Targeting in Thermophiles and Its Application in Clostridium thermocellum, PloS one 8 (7), e69032

19. J Zhou, Y Jiang, Y Deng, Z Shi, B Zhou, K Xue, L Wu, Z He and Y Yang (2013), Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities, mBio 4 (3) 

20. J Zhou, W Liu, Y Deng, YH Jiang, K Xue, Z He, JD Van Nostrand, L Wu, Y Yang and A. Wang (2013), Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community, mBio 4 (2)

21. Y Zhang, Z Lu, S Liu, Y Yang, Z He, Z Ren, J Zhou and D Li (2013), Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau, BMC microbiology 13 (1), 72

22. Y. Deng, Y. Jiang, Y. Yang, Z. He, F. Luo and J. Zhou (2012), Molecular ecological network analyses, BMC Bioinformatics 13:113

23. Y. Li, T. Tschaplinski, N. Engle, C. Hamilton, M. Rodriguez, J. Liao, C. Schadt, A. Guss, Y. Yang and D. Graham (2012), Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations, Biotechnology for Biofuels 5:2-2

24. J Lin, J Zuo, R Ji, X Chen, F Liu, K Wang, Y Yang (2012), Methanogenic community dynamics in anaerobic co-digestion of fruit and vegetable waste and food waste, Journal of Environmental Sciences 24 (7), 1288-1294

25. J. Zhou, L. Wu, Y. Deng, X. Zhi, Y. Jiang, Q. Tu, J. Xie, J. D. Van Nostrand, Z. He and Y. Yang (2011), Reproducibility and Quantitation of Amplicon Sequencing-based Detection. The ISME Journal 5: 1303-1313

26. W. Higashide, Y. Li, Y. Yang and J. Liao (2011), Metabolic Engineering of Clostridium cellulolyticum for Production of Isobutanol from Cellulose, Applied and Environmental Microbiology 77(8): 2727-2733

27. J. Zhou, Y. Deng, F. Luo, Z. He and Y. Yang (2011) Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2, mBio 2(4): e00122-11

28. Y. Yang*, L. A. McCue, A. B. Parsons, S. Feng and J. Zhou (2010), The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control. BMC Microbiology 10:264

29. C. Hemme, Y. Yang, J. Zhou et al., Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production (2010). J. Bacteriol. 192(24): 6494-6496

30. H. Gao, S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K. Nealson, J. Fredrickson, J. Tiedje, M. Romine, J. Zhou (2010), Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration, Microbial Biotechnology 3(4): 455-466

31. X. Zhang, Z. Zhang, Z. Zhu, N. Sathitsuksanoh, Y. Yang and P. Zhang (2010), A Highly-Active Family 48 Cellobiohydrolase from Clostridium phytofermentans ISDg: Heterologous Expression in Escherichia coli and Bacillus subtilis, Characterization, and Processivity. Appl. Microbiol. Biotechnol 86(2):525-533

32. Y. Yang*, D. P. Harris, F. Luo, W. Xiong, M. Joachimiak, L. Wu, P. Dehal, J. Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin and J. Zhou (2009), Snapshot of Iron Response in Shewanella oneidensis by Gene Network Reconstruction, BMC Genomics 10:131

33. Y. Yang* (2009) Use of Genomic DNA as Reference in DNA Microarrays, Micro and Nano Technologies in Bioanalysis, 439-450

34. Y. Yang*, M. Zhu, L. Wu and J. Zhou (2008) Assessment of Data Processing to Improve Reliability of Microarray Experiments Using Genomic DNA Reference, BMC Genomics 9(S2):S5.

35. Y. Yang*, D. P. Harris, F. Luo, L. Wu, A. B. Parsons, A. V. Palumbo and J. Zhou (2008) Physiological and Transcriptomic Analyses to Characterize the Function of Fur and Iron Response in Shewanella oneidensis, BMC Genomics 9(S1):S11.

36. F. Luo, Y. Yang, J. Zhong, H. Gao, L. Khan, D. K. Thompson and J. Zhou (2007) Constructing Gene Co-expression Networks and Predicting Functions of Unknown Genes by Random Matrix Theory, BMC Bioinformatics 8:299. (co-first author)

37. F. Luo, Y. Yang, C. Chen, R. Chang, J. Zhou and R. Scheuermann (2007) Modular Organization of Protein Interaction Networks, Bioinformatics 23(2):207-214.

38. Y. Yang*, M. Zhu, L Wu, J Zhou (2007) Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays, Bioinformatics and Bioengineering 7: 593-600

39. M. Zhu, Q. Wu, Y. Yang and J. Zhou (2006) A New Approach to Identify Functional Modules Using Random Matrix Theory, Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 1:117-123.

40. F. Luo, J. Zhong, Y. Yang, R. Scheuermann and J. Zhou (2006) Application of Random Matrix Theory to Biological Networks Physics Letter A 357(6): 420-423.

41. F. Luo, J. Zhong, Y. Yang and J. Zhou (2006) Application of random matrix theory to microarray data for discovering functional gene modules, Physical Review E. 73, 031924.

42. S. D. Brown, M. Martin, S. Deshpande, S. Seal, K. Huang, E. Alm, Y. Yang, L. Wu, T. Yan, X. Liu, A. Arkin, K. Chourey, J. Zhou and D. K. Thompson (2006) Cellular Response of Shewanella oneidensis to Strontium Stress, Applied and Environmental Microbiology 72(1), 890-900.

43. Y. Yang and U. T. Meier (2003) Genetic interaction between a chaperone of small nucleolar ribonucleoprotein particles and cytosolic serine hydroxymethyltransferase,  Journal of Biological Chemistry 278(26), 23553-23560.

44. Y. Yang, C. Isaac, C. Wang, F. Dragon, V. Pogacic & U. T. Meier (2000) Conserved composition of mammalian box H/ACA and box C/D small nucleolar ribonucleoprotein particles and their interaction with the common factor Nopp140, Molecular Biology of the Cell 11, 567-577.

45. C. Isaac, Y. Yang& U. T. Meier (1998) Nopp140 functions as a molecular link between the nucleolus and coiled bodies, Journal of Cell Biology 142, 319-329.

申请专利、注册软件:

美国专利appln. No. 12/233,806 Methods for targeted mutagenesis in biomass-degrading bacteria第一发明人

美国专利appln. No. 61/150,097 Transformation of Gram Positive Bacteria by Sonoporation第一发明人,已授权