IEG Members:Ye Deng

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Curriculum Vitae
Basic information
Name: Ye Deng
Title: Research Scientist
Nationality: China
Major field: Bioinformatics and ecology
Current address: Institute for environmental Genomics,
Stephenson Research & Technology Center
101 David L. Boren Blvd.
Norman, OK 73019
Telephone: 405-325-3052(office)

Professional Background
Aug.2009-present: Research scientist
Jul.2007-Aug.2009: Post-doctoral Research Assoc. of University of Oklahoma
Supervisor: Dr. Jizhong, Zhou
Dec.2005-Jun.2007: Exchange visitor of Michigan State University,
work in Oklahoma University
Supervisor: Dr. Jizhong, Zhou
Jan.2004-Jun.2007: Ph.D. Biochemistry and Molecular Biology, Zhejiang University, P.R.China
Supervisor: Prof. Debao, Li
Sept.2002-Dec.2003: M.S. Biochemistry and Molecular Biology, Zhejiang University, P.R.China
Supervisor: Dr. Haitao, Dong
Sept.1998-Jun.2002: B.S. Applied Chemistry, College of Chemistry and Chemical Engineering, Central South University, P.R.China

Recent Publications
Deng Y., Jiang Y., Yang Y., He Z., Luo F., Zhou J. 2012. Molecular Ecological Network Analyses. BMC Bioinformatics, 13(1):113.
Liang Y., Van Nostrand J., NGuessan L., Peacock A., Deng Y., Long P., Resch C., Wu L., He Z., Li G., HAZEN T., Lovley D., Zhou J.. Microbial Functional Gene Diversity with a Shift of Subsurface Redox Condition during in situ Uranium Reduction. Appl. Environ. Microbiol,78(8):2966-72.
Deng Y., He Z., Xu M., Qin Y., Van Nostrand J., Wu L., Roe B., Wiley G., Hobbie S., Reich P., Zhou J. 2012. Elevated carbon dioxide alters the structure of soil microbial communities. Appl. Environ. Microbiol, 78(8):2991-5.
He, Z., Y. Deng, and J.-Z. Zhou. 2011. Development of functional gene microarrays for microbial community analysis. Curr. Opin. Microbiol.
Zhou J., K. Xue, J. Xie, Y. Deng, L. Wu, X. Cheng, S.Fei, S. Deng, Z.He, J.D. Van Nostrand, and Y. Luo. 2012. Microbial mediation of carbon-cycle feedbacks to climate warming. Nat. Clim. Change. 2, 106–110
Lu, Z., Y. Deng, J.D. Van Nostrand, Z. He, J. Voordeckers,A. Zhou, Y. Lee, O.U. Mason, E.A. Dubinsky, K.L. Chavarria, L.M. Tom, J.L. Fortney, R. Lamendella, J.K. Jansson, P. D’haeseleer, T.C. Hazen and J. Zhou. 2012. Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. The ISME J. doi:10.1038/ismej.2011.91
Christopher L. Hemme, Matthew W. Fields, Qiang He, Ye Deng, Lu Lin, Qichao Tu, Housna Mouttaki, Aifen Zhou, Xueyang Feng, Zheng Zuo, Bradley D. Ramsay, Zhili He, Liyou Wu, Joy Van Nostrand, Jian Xu, Yinjie J. Tang, Juergen Wiegel, Tommy J. Phelps, and Jizhong Zhou. 2011. Correlation of genomic and physiological traits to biofuel yields in Thermoanaerobacter species. Appl. Environ. Microbiol, 77:7998-8008.
He, Z., D. J. Van Nostrand, Y. Deng, and Z.-J. Zhou. 2011. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front. Environ. Sci. Engin. China 5: 1-20.
Deng Y.*, Zhou J.*, Luo F., He Z. , Yang Y., 2011. Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2. mBio, 2(4):e00122-11. * co-first authors
Liang, Y.T. J. D. van Nostrand, Y. Deng, Z.H. He, L.Y. Wu, X. Zhang, G.H. Li and J.-Z. Zhou. 2011. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. The ISME J. 5, 403-413.
Xie J., He Z., Liu X., Liu X.D, Van Nostrand J.D., Deng Y., Wu L., Zhou J., Qiu G. 2011. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl Environ Microbiol. 77(3): 991-9
Van Nostrand*, J.D., L.Y. Wu*, W.-M. Wu, Z.J. Huang, T. J. Gentry, Y. Deng, J. Carley, S. Carroll, Z.-H. He, B.H. Gu, J. Luo, C. S. Criddle, D. B. Watson, P. M. Jardine, T. L. Marsh, J.M. Tiedje, T. C. Hazen, and J.Z. Zhou. 2011. Dynamics of microbial community functional structure visualized by GeoChip during the in-situ bioremediation of a uranium-contaminated aquifer. Appl. Environ. Microbiol, 77:3860-3869
Zhili He, Yvette Piceno, Ye Deng, Meiying Xu, Zhenmei Lu, Todd DeSantis, Gary Andersen, Sarah E Hobbie, Peter B Reich and Jizhong Zhou. 2011. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. The ISME Journal 2011:1-14.
Zhou, J-.Z. *, L.-Y. Wu*, Y. Deng, X.-Y. Zhi, Y.-H. Jiang, Q.-C. Tu, J.-P. Xie, J. D. Van Nostrand, Z.-H. He, and Y.-F. Yang. 2011. Reproducibility and quantitation of amplicon sequencing-based detection. The ISME J, doi: 10.1038/ismej.2011.11.
Wang AJ, Liu WZ, Deng Y, Van Nostrand JD, Zhou JZ. Multiple community states of planktonic communities on functional gene structure in microbial electrolysis cell (MEC).. J Biotech. 2010, 150: S239-S240
Epelde L, Becerril JM, Kowalchuk GA, Deng Y, Zhou J, Garbisu C. 2010. Impact of metal pollution and thlaspi caerulescens growth on soil microbial communities. Applied and Environmental Microbiology, 2010, 76: 7843-7853
Deng Y*, Zhou J*, Luo F, He Z, Tu Q, Zhi X. 2010. Functional molecular ecological networks. mBio, 2010, 1(4). pii: e00169-10. *equally contribution
Hazen TC, Dubinsky EA, Desantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad MS, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU. 2010. Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria. Science, 2010, 330: 204-208
Zhou, A.-F, Z.H. He, A. M. Redding, A. Mukhopadhyay, C. L. Hemme, M. P. Joachimiak, F. Luo, Y. Deng, K. S. Bender, J. D. Keasling, D. A. Stahl, M. W Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J.-Z. Zhou. 2010. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol, 12(10):2645-57.
Deng Y.*, He Z.*, Wu L., Van Nostrand J.D., Zhou J. GeoChip 3.0 as a high throughput tool for analyzing microbial community functional structure. ISME Journal, 2010, doi:10.1038/ismej.2010.46. *equal contribution
He Z., Xu M., Deng Y., Kang S., Kellogg L., Wu L., Van Nostrand, J., Hobbie S., Reich P., Zhou J., Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecology Letter, 2010, 13(5):564-75.
Hemme C.L., Deng Y., Gentry T.J., Fields M.W., Wu L., Barua S., Barry K., Green-Tringe S., Watson D.B., He Z., Hazen T.C., Tiedje J.M., Rubin E.M. and Zhou J., Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 2010; 4(5):660-72.
Liang Y., He Z., Wu L., Deng Y., Li G. and Zhou J. Development of a universal standard for microarray data comparison across different microbial communities, Applied and Environmental Microbiology 2010; 76: 1088-1094
15. Liu, W.Z., A.J. Wang, Sh. Cheng, B. E. Logan, H. Yu, Y. Deng, J. D. van Nostrand, L.Y. Wu, Z.H. He and J.-Z. Zhou. 2010. Geochip-based Geochip-Based Functional Gene Analysis of Anodophilic Communities in Microbial Electrolysis Cells under Different Operational Modes. Environ. Sci. & Technol., 44: 7729-7735.
Xu Meiying, Wei-Min Wu, Liyou Wu, Zhili He, Joy D Van Nostrand, Ye Deng, Jian Luo, Jack Carley, Matthew Ginder-Vogel, Terry J Gentry, Baouhua Gu, David Watson, Philip M Jardine, Terence L Marsh, James M Tiedje, Terry Hazen, Craig S Criddle and Jizhong Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. The ISME Journal. doi: 10.1038/ismej.2010.31.
Zhou, J., Z. He, J. D. Van Nostrand, L.Y. Wu, and Y. Deng. 2010. Applying GeoChip Analysis to Disparate Microbial Communities. Microbes, 5:60-65.
Jin Q., Chen B., Li Y., Peng Y., Deng Y., Dai C., Luo H., Zhao D., Chen J., Li D. and Dong H. Expression Profile During the Development of Appressoria Induced by Hydrophobic Surfaces in Magnaporthe grisea Y34. Journal of Phytopathology 2009;
Liang Y., Li G., Van Nostrand J.D., He Z., Wu L.,Deng Y., Zhang X. and Zhou J. Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiology Ecology 2009; 70: 324-333.
Joy D. Van Nostrand, Wei-Min Wu, Liyou Wu, Ye Deng, Jack Carley, Sue Carroll, Zhili He, Baohua Gu, Jian Luo, Craig S. Criddle, David B. Watson, Philip M. Jardine, Terence L. Marsh, James M. Tiedje, Terry C. Hazen, Jizhong Zhou. GeoChip-based analysis of functional microbial communities in a bioreduced uranium-contaminated aquifer during reoxidation by oxygen. Environmental Microbiology. 2009
Fengping Wang, Huaiyang Zhou, Jun Meng, Xiaotong Peng, Lijing Jiang, Ping Sun, Chuanlun Zhang, Joy D. Van Nostrand, Ye Deng, Zhili He, Liyou Wu, Jizhong Zhou, and Xiang Xiao. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. PNAS. 2009, 106(12): 4840
Ye Deng, Zhili He, Joy D Van Nostrand and Jizhong Zhou. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics. 2008, 9: 491
Jinjie Shanga, Xiaosong Wu, Xiuwan Lan, Yunyan Fan, Haitao Dong, Ye Deng, Donald L. Nuss and Baoshan Chen. Large-scale expressed sequence tag analysis for the chestnut blight fungus Cryphonectria parasitica. Fungal Genetics and Biology. 2008, 45(3)
Jin Q., Dong H., Peng Y., Chen B., Shao J., Deng Y., Dai C., Fang Y., Lou Y., Li Y. and Li D., Application of cDNA array for studying the gene expression profile of mature appressoria of Magnaporthe grisea. Journal of Zhejiang University SCIENCE - 2006; 8: 88-97
Ye Deng*, Haitao Dong*, Jack Chen, Sheng Wang, Sihua Peng, Cheng'en Dai, Yongqi Fang, Jing Shao, Yichun Lou and Debao Li. exploration of 3′-end processing signals and their tissue distribution in Oryza sativa. GENE. 2007, 389: 107-113
  • These authors contributed equally to this work
Ye Deng, Haitao Dong, Qingchao Jin, Cheng’en Dai, Yongqi Fang, Shen Liang, Ke Wang, Jing Shao, Yichun Lou, Wenqin Shi, Demetrios J. Vakalounakis, Debao Li. Analysis of EST data and gene expression profiles in the conidial development of Fusarium oxysporum. Applied and Environmental Microbiology. 2006, 72: 1667-1671
Xiaoqin Guo, Haitao Dong, Kangle Zheng, Hongmei Lou, Xuelin Tan, Yongqi Fang, Yanqin Wang, Ye Deng, Chengen Dai, Yichun Lou, Jing Shao, Wenqin Shi, Dong Zhao, Debao Li. Gene Expression Profiling under Different Photoperiod/Temperature Conditions in a Photoperiod-/Thermo- Sensitive Genic Male Sterile Line of Rice (Oryza sativa L.). Chinese Science Bulletin. 2005, 50(22): 2509-2513
Haitao Dong, Wenzheng Li, Sandra Perez Alvarez, Hongmei Luo, Ye Deng, Qingchao Jin, Chen’en Dai, Daniel Cabezas Montero, Yongqi Fang, Jing Shao, Yichun Lou, Wenqin Shi, Yan Shao, Yongping Li, Jack Chen, Debao Li. Large-scale identification of ESTs from Nicotiana tabacum by normalized cDNA library sequencing. Medical Hypotheses Research. 2005, 3: 418-496
Li-Hua Wang, Ye Deng, Yong-Qi Fang, Xue-Lin Tan, De-Bao Li. Monitoring and Analyzing the Genes Specific-Expressed at Flowering Stage of Rice (Oryza sativa). Chinese Journal of Rice Science. 2004, 18(3): 192-198.

Research Awards
Zhou J., He Z., Wu L., Van Nostrand J.D.,Deng Y., OU GeoChip3. R&D 100 Awards 2009.
2010 Innovator of the Year award.

Other skills
Certified the Microsoft Certified Systems Engineer (MCSE) in 2002
Referee of basketball
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