清华大学环境学院

School of Environment

 

Name
YANG Yunfeng
Division Division of Environmental Biology
Position Professor
Address
School of Environment, Tsinghua University, Beijing 100084, P.R.China 
Telephone  +86-10-62784692
E-mail  yangyf@tsinghua.edu.cn
Facsimile  +86-10-62785687

Education background

Albert Einstein College of Medicine                         Ph.D.                2003             Microbiology

City University of New York                                        M.S.                   2002             Computer Sciences

University of Science & Technology of China        B.S.                   1996              Biology

Experience

RESEARCH AND PROFESSIONAL EXPERIENCE

2010-present  Professor, School of Environment, Tsinghua University

2006-2010  Staff Scientist, Biosciences Division, Oak Ridge National Laboratory

2006-2009  Residential faculty for Oak Ridge Science Semester Program, Denison University

2003-2006  Postdoctoral Research Associate, Environmental Sciences Division,

                      Oak Ridge National Laboratory

TEACHING EXPERIENCE

● Lecturer: Principles and Techniques of Modern Environmental Microbiology Monitoring (2014-Current)

● Lecturer: Advanced Microbiology (2013-Current)

● Lecturer of Course BIOL325: Genetics (2007-2009)

● Lecturer of Course BIOL201: Cell and Molecular Biology (2006)

Concurrent Academic

• Associate Editor of BMC Microbiology, 2014-Current

• Editorial board member of Applied and Environmental Microbiology, 2013-2015

• Proposal reviewer of U.S. Department of Energy SBIR/STTR program, 2007-2010

• Editorial board member of International Journal of Functional Informatics and Personalised Medicine, 2007-2009

Areas of Research Interests/ Research Projects

Elucidation of microbe-mediated biogeochemistry via metagenomics approaches. Major focuses are to understand (a) how environmental changes affect structural genes of microbial communities and (b) how microbial genes mediate biogeochemical cycles

Honors And Awards

• Early Career Award, Tsinghua University, 2014 - The highest award of Tsinghua University for young scientists

• Outstanding Scientific Achievement Award, School of Environment, Tsinghua University, 2013

Academic Achievement

PATENTS

• U.S. Patent appln. No. 61/150,097 Principle inventor, 2009

• U.S. Patent appln. No. 12/233,806 Methods for targeted mutagenesis in biomass-degrading bacteria. Principle inventor, allowed in 2013.

PUBLICATIONS

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.