| 姓 名： | 楊云鋒 |
| 所在單位： | 生態(tài)學(xué)教研所 |
| 職 稱： | 正高級 |
| 郵寄地址： | 清華大學(xué)環(huán)境學(xué)院 |
| 辦公電話： | 010- 62784692 |
| 電子郵件： | yangyf@tsinghua.edu.cn |
| 辦公地點(diǎn)： | 環(huán)境節(jié)能樓925室 |
教育背景
1996. 8 – 2003. 1 美國Albert Einstein College of Medicine生物專業(yè)，博士
2000. 1 – 2002. 5 美國City University of New York計(jì)算機(jī)專業(yè)，碩士 (第二學(xué)位)
1991. 9 – 1996. 7 中國科大生物系，學(xué)士
工作履歷
2011.01-現(xiàn)在 清華大學(xué)環(huán)境學(xué)院，教授
2010.09-2011.01 清華大學(xué)環(huán)境科學(xué)與工程系，教授
2006.03-2010.09 美國橡樹嶺國家實(shí)驗(yàn)室生命科學(xué)部，研究員（staff scientist）
2006.08-2009.12 美國DENISON 大學(xué)，兼職教授（part-time professor）
2003.02-2006.03 美國橡樹嶺國家實(shí)驗(yàn)室環(huán)境科學(xué)部，博士后
教學(xué)：
本科課程Course BIOL325: Genetics (2007-2009)
本科課程Course BIOL201: Cell and Molecular Biology (2006)
學(xué)術(shù)兼職
Applied and Environmental Microbiology 雜志編委（2012-至今）
美國能源部 SBIR/STTR 項(xiàng)目評審（2007-2010）
International Journal of Functional Informatics and Personalised Medicine 雜志編委（2007-2009）
研究領(lǐng)域
科學(xué)類（70%）
1. 與全球氣候變化相關(guān)的環(huán)境微生物群落結(jié)構(gòu)、多樣性、功能的解析和調(diào)控
2. 生物功能基因網(wǎng)絡(luò)的構(gòu)建和解析
工程類 （30%）
1. 應(yīng)用環(huán)境微生物的油氣礦藏勘探新技術(shù)
2. 污水、固廢處理處置的微生物過程研究
3. 生物能源、污染場地生物修復(fù)的微生物資源開發(fā)和基因工程改造
研究概況
近年主持或者參與主持的科研項(xiàng)目：
1. 凍土帶天然氣水合物微生物勘查技術(shù)子課題（中國科技部863項(xiàng)目，2012-2015）
2. 環(huán)境多因子對溫帶草原土壤微生物群落結(jié)構(gòu)的影響（國家基金委面上項(xiàng)目，2012-2015）
3. 基于宏基因組學(xué)技術(shù)的工程系統(tǒng)微生物群落特征研究（國家重點(diǎn)實(shí)驗(yàn)室自主項(xiàng)目，2011-2013）
4.能源部生物能源中心梭菌遺傳工程項(xiàng)目（美國能源部GTL項(xiàng)目, 2007 – 2012)
5. 楊樹–微生物相互作用項(xiàng)目，分離微生物和遺傳工程開發(fā)子課題（美國能源部GTL項(xiàng)目2009 – 2012）
6. 土壤微生物分布、轉(zhuǎn)移過程中細(xì)胞膠結(jié)的定量分析子課題 (美國能源部ERSP exploratory項(xiàng)目2010 – 2011)
7.對重金屬污染的地下水中分離和篩選功能微生物項(xiàng)目，分離微生物子課題（美國能源部ERSP項(xiàng)目，2007 – 2010）
8. 系統(tǒng)生物學(xué)方法理解植物抗旱性機(jī)理項(xiàng)目，功能基因組學(xué)分析和生物網(wǎng)絡(luò)構(gòu)建子課題（美國橡樹嶺國家實(shí)驗(yàn)室LDRD項(xiàng)目，2007 – 2010）
9. 合成氣-醇類轉(zhuǎn)換細(xì)菌的遺傳工程開發(fā)（美國橡樹嶺國家實(shí)驗(yàn)室LDRD項(xiàng)目，2007 – 2010）
10. 食品生產(chǎn)過程中檢測沙門氏菌的新型技術(shù)（Mars, Inc. 資助項(xiàng)目和美國橡樹嶺國家實(shí)驗(yàn)室Seed money項(xiàng)目2009 – 2010）
11. Shewanella Federation 還原金屬分子機(jī)制子課題（美國能源部GTL項(xiàng)目，2006 – 2008）
12. 生物能源梭菌的遺傳工程開發(fā)（美國橡樹嶺國家實(shí)驗(yàn)室Seed money項(xiàng)目, 2006 – 2007）
學(xué)術(shù)成果
發(fā)表文章：
近五年論文引用次數(shù)300余次，H指數(shù)為11。
1. Y. Deng, Y. Jiang, Y. Yang, Z. He, F. Luo and J. Zhou (2012), Molecular Ecological Network Analyses BMC Bioinformatics 2012, 13:113
2. 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.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. ISME J 5: 1303-1313
3.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
4.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
5.Y. Yang, L. A. McCue, A. B. Parsons, S. Feng and J. Zhou (2010), Thetricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control. BMC Microbiology 10:264
6.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
7.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
8.X. Zhang, Z. Zhang, Z. Zhu, N. Sathitsuksanoh, Y. Yang and P. Zhang (2009), A Highly-Active Family 48 Cellobiohydrolase from Clostridium phytofermentansISDg: Heterologous Expression in Escherichia coli and Bacillus subtilis, Characterization, and Processivity. Appl. Microbiol. Biotechnol 86(2):525-533
9.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
10.Y. Yang (2009) Use of Genomic DNA as Reference in DNA Microarrays, Methods Molecular Biology, Vol. 544, chapter 29.
11.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.
12.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.
13.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)
14.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.
15.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.
16.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.
17.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.
18.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.
19.Y. Yang and U. T. Meier (2003) Genetic interaction between a chaperone of small nucleolarribonucleoprotein particles and cytosolic serine hydroxymethyltransferase, Journal of Biological Chemistry 278(26), 23553-23560.
20.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 nucleolarribonucleoprotein particles and their interaction with the common factor Nopp140, Molecular Biology of the Cell 11, 567-577.
21.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.
申請專利、注冊軟件：
美國專利appln. No. 12/233,806 Methods for targeted mutagenesis in biomass-degrading bacteria.第一發(fā)明人
美國專利appln. No. 61/150,097 Transformation of Gram Positive Bacteria by Sonoporation.第一發(fā)明人
