IEG Members:Qichao Tu

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Qichao Tu

Birth: August 1984

Gender: Male

Phone: 405-509-5432

Email: qichao AT ou.edu

Adress: 101 David L Boren Blvd, Norman, OK 73019


RESEARCH INTERESTS

Microbial Ecology, Metagenomics, Next Generation Sequencing, Microarrays, Bioinformatics


COMPUTER SKILLS

Master level: PERL, R, MYSQL, UNIX


EDUCATION

University of Oklahoma

Ph.D. in Microbiology 2008~2014

Dissertation: Metagenomic Insights into Microbial Community Responses to Long-term Elevated CO2

Zhejiang University

M.S. in Biochemistry and Molecular Biology 2006~2008

Thesis: Bioinformatics analysis of 3' end untranslated region in Magnaporthe grisea and signicantly expressed genes in rice endosperm

Zhejiang university

B.S. in Bioinformatics 2002~2006

Thesis: Prediction of in vivo drug target protein for natural products


RESEARCH EXPERIENCE

Postdoctoral Research Associate, Institute for Environmental Genomics, University of Oklahoma 2014~present

Visiting Scholar, Metagenomics Team, BioScience Division, Los Alamos National Lab 2010~2011

Visiting Scholar, Institute for Environmental Genomics, University of Oklahoma 2007~2008


AWARDS

2014 ASM General Meeting Outstanding Student Poster

2011 DOE Genomic Science Meeting Student Travel Grant

2011, 2014 ASM General Meeting Student Travel Grant

2010, 2012, 2013 IEG Scholarship


PROFESSIONAL TALKS

2011 DOE Genomic Sciences Meeting Washington D.C. From Community Structure to Functions: Metagenomics-enabled Predictive Understanding of Temperature Sensitivity of Soil Carbon Decomposition to Climate Warming


PUBLICATIONS

1. Qichao Tu, Mengting Yuan, Zhili He, Ye Deng, Kai Xue, Liyou Wu, Sarah E. Hobbie, Peter B. Reich, and Jizhong Zhou. Fungal communities respond to long-term elevated CO2 by community reassembly. (submitted)

2. Qichao Tu, Zhili He, and Jizhong Zhou. "Strain/species identification in metagenomes using genome-specific markers". Nucleic acids research 42.8 (2014): e67-e67. (Editor's pick by Genomeweb)

3. Qichao Tu, Zhili He, Yan Li, Yanfei Chen, Ye Deng, Lu Lin, Christopher L. Hemme, Tong Yuan, Joy Van Nostrand, Liyou Wu, Xuedong Zhou, Wenyuan Shi, Lanjuan Li, Jian Xu, Jizhong Zhou. “Development of HuMiChip for Functional Profiling of Human Microbiomes.”PloS one 9.3 (2014): e90546.

4. Qichao Tu, Zhili He, Ye Deng and Jizhong Zhou. “Strain/Species-Specific Probe Design for Microbial Identification Microarrays.” Applied and environmental microbiology 79.16 (2013): 5085-5088.

5. Qichao Tu, Hao Yu, Zhili He, Ye Deng, Liyou Wu, Joy D. Van Nostrand, Aifen Zhou, James Voordeckers, Yong-Jin Lee, Yujia Qin, Christopher L. Hemme, Zhou Shi, Kai Xue, Tong Yuan, Aijie Wang, and Jizhong Zhou. “GeoChip 4: a functional gene array-based high throughput environmental technology for microbial community analysis." Molecular Ecology Resources. DOI:10.1111/1755-0998.12239 (in press)

6. Qichao Tu, Ye Deng, Jizhong Zhou, and Zhili He. “Development and Evaluation of Functional Gene Arrays with GeoChip as an Example.”Microarrays: Current Technology, Innovations and Applications. Caister Academic Press, Norwich, UK.ISBN: 978-1-908230-49-2 (Book Chapter, in press)

7. Tu, Qichao, Haitao Dong, Haigen Yao, Yongqi Fang, Cheng'en Dai, Hongmei Luo, Jian Yao, Dong Zhao, and Debao Li. "Global identification of significantly expressed genes in developing endosperm of rice by expression sequence tags and cDNA array approaches."Journal of Integrative Plant Biology 50, no. 9 (2008): 1078-1088.

8. Chengwei Luo, Luis Rodriguez-R., Eric Johnston, Liyou Wu, Lei Cheng, Kai Xue, Qichao Tu, Ye Deng, Zhili He, Zhou Shi, mengting Yuan, Sherry Rebecca, dejun Li, Yiqi Luo, E.A.G. Schuur, Patrick Chain, James Tiedje, Jizhong Zhou, and Konstantinos Konstantinidis. “Soil microbial community responses to a decade of warming as revealed by comparative metagenomics”. Applied and environmental microbiology 80.5 (2014): 1777-1786.

9. Meiying Xu, Yun Fang, Jun Liu, Xingjuan Chen, Guoping Sun, Jun Guo, Zhengshuang Hua, Qichao Tu, Liyou Wu, Jizhong Zhou, and Xueduan Liu. Draft genome sequence of Shewanella decolorationis S12, a dye degrading bacterium isolated from a waste-water treatment plant. Genome announcements 1.6 (2013): e00993-13.

10. Lu Lin, Yuetong Ji, Qichao Tu, Ranran Huang, Lin Teng, Xiaowei Zeng, Houhui Song, Kun Wang, Qian Zhou, Yifei Li, Qiu Cui, Zhili He, Jizhong Zhou, and Jian Xu. "Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in thermophiles". Biotechnology for biofuels 6.1 (2013): 103.

11. Fang YANG, Kang NING, Xingzhi CHANG, Xiao YUAN, Yue ZHANG, Xinping CUI, Qichao TU, Yuan TONG, Ye DENG, Christopher L Hemme, Joy Van Nostrand, Zhili HE, Jian Xu. "Saliva microbiota carry caries-specific functional gene signatures." PloS one 9.2 (2014): e76458.

12. Zhou, Aifen, He, Zhili, Qin, Yujia, Lu, Zhenmei, DENG, Ye, Tu, Qichao, Hemme, Christopher, Van Nostrand, Joy, Wu, Liyou, Hazen, Terry, Arkin, Adam, Zhou, Joe. “StressChip as a High Throughput Tool for Assessing Microbial Community Stability.” Environmental science & technology 47.17 (2013): 9841-9849.

13. Dongru Qiu, Hehong Wei, Qichao Tu, Yunfeng Yang, Ming Xie, Jingrong Chen, Mark Pinkerton, Yili Liang, Zhili He, and Jizhong Zhou. “Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1.” Applied and environmental microbiology 79.17 (2013): 5250-5257.

14. Lee, Y.-J., J. D. Van Nostrand, Q. Tu, T. Yuan, L. Cheng, Z. Lu, Y. Deng, M. Q. Carter, Z. He, L. Wu, F. Yang, J. Xu, and J. Zhou. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. The ISME journal 7.10 (2013): 1974-1984.

15. Zhou, Jizhong, Liyou Wu, Ye Deng, Xiaoyang Zhi, Yi-Huei Jiang, Qichao Tu, Jianping Xie, Joy D. Van Nostrand, Zhili He, and Yunfeng Yang. "Reproducibility and quantitation of amplicon sequencing-based detection." The ISME Journal 5, no. 8 (2011): 1303-1313.

16. Hemme, Christopher L., Matthew W. Fields, Qiang He, Ye Deng, Lu Lin, Qichao Tu, Housna Mouttaki et al. "Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields." Applied and Environmental Microbiology 77, no. 22 (2011): 7998-8008.

17. Lin, Lu, Houhui Song, Qichao Tu, Yujia Qin, Aifen Zhou, Wenbin Liu, Zhili He, Jizhong Zhou, and Jian Xu. "The thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria." PLoS Genetics 7, no. 10 (2011): e1002318.

18. Zhou, Jizhong, Ye Deng, Feng Luo, Zhili He, Qichao Tu, and Xiaoyang Zhi. "Functional molecular ecological networks." MBio 1, no. 4 (2010).

19. He, Zhili, Ye Deng, Joy D. Van Nostrand, Qichao Tu, Meiying Xu, Christopher L. Hemme, Xingyuan Li et al. "GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity." The ISME Journal 4, no. 9 (2010): 1167-1179.

20. Dong, HaiTao, XiaoQin Guo, YanXi Pei, ChengEn Dai, YongQi Fang, Qichao Tu, JieYun Zhuang, Dong Zhao, KangLe Zheng, and DeBao Li. "Multiple splicing types of OsRIX4, an RAD21 homolog in rice (Oryza sativa L.)." Chinese Science Bulletin 52, no. 11 (2007): 1468-1474.

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