General

Jian Xu, PhD, Professor and Director of BioEnergy Genome Center, CAS-QIBEBT
E-mail: 
xujian@qibebt.ac.cn
Address: 
No.189 Songling Road , Laoshan District , Qingdao
Website: 
http://www.single-cell.cn/ 

http://www.qibebt.cas.cn/

Research Areas

​XU Jian (xujian@qibebt.ac.cn) currently serves as Director of Single-Cell Center, Director of BioEnergy Division and Assistant Director General at CAS-QIBEBT. He was born in Zhangzhou, Fujian, China in 1976. He obtained B.S in Biotechnology from Peking University in 1997, and M.S. in Computer Science and PhD in Biochemistry under Jeffrey Gordon from Washington University in St. Louis in 2003. After serving as Research Instructor at Genome Institute of Washington University, he joined Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (CAS-QIBEBT) in 2008 and has been the founding Director of Single-Cell Center, CAS-QIBEBT. Jian has published over 140 papers on leading journals such as Science, Cell Host & Microbe, Nature Communications, Science Advances, PNAS, PLoS Biology, PLoS Genetics, ISME J, mBio, Anal Chem, Lab Chip etc, with ~ 12,000 citations (H-index 50). He is a senior editor of mSystems and also served at the Editorial Board of Algal Research and Appl Env Microbiol. His contribution was recognized by a number of career awards from NSFC, MOST and CAS, including National Distinguished Young Scholars Award (2014), National Young-Scientist Award for Science and Technology (2016) and VCANBIO Award for Biosciences and Medicine (2016). He has mentored nearly 20 doctoral students and postdoctoral scholars, and was recognized for excellence in mentorship via the 2013 CAS 100 Best Doctoral Thesis Mentor Award and the 2014 UCAS-BHPB Mentorship Award. 

Single-Cell Center consists of over 90 specialists from single-cell genomics, synthetic biology, microfluidics, bioinformatics, optical engineering and precision instrumentation. We have introduced novel concepts for single-cell metabolic phenomes such as ‘ramanome’, ‘meta-ramanome’ and ‘MIC-MA’. We invented the Single-cell Analysis Instrument Series, including Ramanome/meta-ramanome Intelligent Analyzer, Raman-Activated Cell Sorter, RACS-Seq, FlowRACS, EasySort, etc). We develop single-cell and metagenomics big-data software such as Microbiome Search Engine (www.mse.ac.cn) and (MP-G)n. These innovations are supporting screening of cell factories, bioresource mining, marine ecological monitoring, diagnosis of chronic diseases, precision antibiotic administration, cancer drug screening, etc. Moreover, the center develops microalgal synthetic biology (using Nannochloropsis oceanica as a model) for scalable CO2 fixation and photosynthetic production of nutriceuticals and biofuels. 

Education

2003-2004 Washington University in St. Louis, School of Medicine, St. Louis, MO. Postdoctoral Scholar, Center for Genome Sciences

1997-2003 Washington University in St. Louis, School of Medicine, St. Louis, MO. Ph.D., Biochemistry(Thesis Advisor: Jeffrey I. Gordon)

2000-2003 Washington University in St. Louis, School of Engineering, St. Louis, MO. M.S., Computer Science

1993-1997 Peking University, Beijing, China. B.S., Biotechnology


Honors & Distinctions

1. “ChineseYoung-Scientist Awardfor Science and Technology(中国青年科技奖)”, 2016, by the Central Governmentof China(中组部)and the Chinese Association of Science and Technology (中国科协)

2. “TaishanScholarsAward(泰山学者)”, 2015, by Shandong Administration of Scienceand Technology

3. “National DistinguishedYoung ScholarsAward(国家杰出青年基金)”, 2014, by National Science Foundation of China

4. “Leadership in Scientific Innovation Award” (中青年科技创新领军人才计划), 2013, by Ministry of Science and Technology of China (科技部)

5. “ExceptionalYoung Talent Award(万人计划之青年拔尖人才)”, 2012, by the Central Governmentof China(中组部)

6. “UCAS-BHPB Award for Excellence in Research Mentorship”(as mentor of my doctoral student Shi Huang),2014, by University of Chinese Academy of Science (CAS) and BHPBilliton.

7. “The 100 Best PhD Thesis Mentoring Award”, as mentor of my first doctoral student Lu Lin, 2013, by CAS.

8. “Leadership in Entrepreneurship and Innovation Award”(青岛市创业创新领军人才), 2013, by Qingdao Municipal Government

9. Innovation in Research Award, 2012, by National Union of Oversea Chinese(中国侨联)

10. Outstanding Graduate-Course Lecturer Award, 2012, by CAS-QIBEBT

11. DistinguishedYoung InvestigatorAward, 2009, by Natural ScienceFoundation of Shandong

12. Hundred Talent Award(****), 2008, by Chinese Academy of Sciences


Publications

1.      Xu Chenggang, Huang Ranran, Teng Lin, Jing Xiaoyan, Hu Jianqiang, Cui Guzheng, Wang Yilin, Cui Qiu, Xu Jian: Cellulosome stoichiometry in Clostridium cellulolyticum is regulated by selective RNA processing and stabilization. Nature Communications. 2015, 6:6900 doi: 10.1038/ncomms7900.

2.      Li Jing, Han Danxiang, Wang Dongmei, Ning Kang, Jia Jing, Wei Li, Jing Xiaoyan, Huang Shi, Chen Jie, Li Yantao, Hu Qiang, Xu Jian: Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oleaginousness in Microalgae. Plant Cell 2014. 10.1105/tpc.113.121418.

3.      Wang Dongmei, Ning Kang, Li Jing, Hu Jianqiang, Han Danxiang, Wang Hui, Zeng Xiaowei, Jing Xiaoyan, Zhou Qian, Su Xiaoquan, Chang Xingzhi, Wang Anhui, Wang Wei, Jia Jing, Wei Li, Xin Yi, Qiao Yinghe, Huang Ranran, Chen Jie, Han Bo, Yoon Kangsup, Hill Russell T., Zohar Yonathan, Chen Feng, Hu Qiang, Xu Jian: Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits. PLoS Genet 2014, 10(1):e1004094.

4.      Lu Yandu, Danuše Tarkowská, Veronika Turečková, Luo Tingwei, Xin Yi, Li Jing, Wang Qintao, Nianzhi Jiao, Strnad Miroslav, Xu Jian:  Antagonistic roles of abscisic acid and cytokinin during response to nitrogen depletion in oleaginous microalga Nannochloropsis oceanica expand the evolutionary breadth of phytohormone function. Plant J, 2014, DOI: 10.1111/tpj.12615.

5.      Wang Tingting, Ji Yuetong, Wang Yun, Li Jing, Huang Shi, Jia Jing, Han Danxiang, Hu Qiang, Huang Wei E, Xu Jian: Quantitative Dynamics of Triacylglycerol Accumulation in Microalgae Populations at Single-Cell Resolution Revealed by Raman Spectrometry. Biotech Biofuels, 2014, 7:58. DOI: 10.1186/1754-6834-7-58.

6.      Lin Lu, Song Houhui, Tu Qichao, Qin Yujia, Zhou Aifen, Liu Wenbin, He Zhili, Zhou Jizhong, Xu Jian: The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria. PLoS Genet 2011, 7(10):e1002318.

7.      Teng Fei, Yang Fang, Huang Shi, Bo Cunpei, Zhengjiang Xu, Amnon Amir, Knight Rob, Ling Junqi, Xu Jian: Prediction of Early Childhood Caries via Spatial-temporal Variation of Oral Microbiota, Cell Host & Microbe, 2015. http://dx.doi.org/10.1016/j.chom.2015.08.005.

8.      Huang Shi, Li Rui, Zeng Xiaowei, He Tao, Zhao Helen, Chang Alice, Bo Cuipei, Chen Jie, Yang Fang, Knight Robin D., Liu Jiquan, Davis Catherine, Xu Jian: Oral Microbial Structure Predicts Gingivitis Susceptibility and Severity. ISME J, 2014.

9.      Yang Fang, Zeng Xiaowei, Ning Kang, Liu Kuan-Liang, Lo Chien-Chi, Wang Wei, Chen Jie, Wang Dongmei, Huang Ranran, Chang Xingzhi, Chain Patrick S., Xie Gary, Ling Junqi, Xu Jian: Saliva Microbiomes Distinguish Caries-Active from Healthy Human Populations. ISME J 2012, 6(1):1-10.

10.  Xu Jian, Mahowald Michael A., Ley Ruth E., Lozupone Catherine A., Hamady Micah, Martens Eric C., Henrissat Bernard, Coutinho Pedro M., Minx Patrick, Latreille Philippe, Cordum Holland, Van Brunt Andrew, Kim Kyung, Fulton Robert S., Fulton Lucinda A., Clifton Sandra W., Wilson Richard K., Knight Robin D., Gordon Jeffrey I.: Evolution of Symbiotic Bacteria in the Distal Human Intestine. PLoS Biol 2007, 5(7):e156.

11.  Xu Jian and Gordon Jeffrey I.: Honor Thy Symbionts. Proc Natl Acad Sci USA 2003, 100(18):10452-10459.

12.  Xu Jian, Bjursell Magnus K., Himrod Jason, Deng Su, Carmichael Lynn K., Chiang Herbert C., Hooper Lora V., Gordon Jeffrey I.: A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis. Science 2003, 299(5615):2074-2076.


Papers

Complete List of Publications by XU Jian

 

Area I. Disease Diagnosis and Prevention via Human Microbiomes

 

1.      Huang Shi, Li Zhen Li, He Tao, Bo Cunpei, Alice Chang, Lin Lin, He Yanyan, Liu Jiquan Liu, Li Rui, Xu Jian, Microbiota-based Signature of Gingivitis Treatments: A Randomized Study, Sci Rep, 2016. 6:24705 | DOI: 10.1038/srep24705.

2.      Fei Teng, Tao He, Shi Huang,Cunpei Bo, Jie Chen, Helen Zhao, Alice Chang, Jiquan Liu, Duane Charbonneau, Jian Xu, Rui Li,Junqi Ling:CPC mouth rinse perturbs dental plaque maturation and alleviates experimental gingivitis, International Journal of Oral Science, in press.

3.      Zhuang Guo, Jiachao Zhang,Zhanli Wang, Kay Ying Ang, Shi Huang, Xiaoquan Su, Qiangchuan Hou, Jianmin Qiao, Yi Zheng, Lifeng Wang, Eileen Koh,Ho Danliang, Jian Xu, Yuan Kun Lee, Heping Zhang,  Intestinal Microbiota Distinguish Gout Patients from Healthy Humans, Sci Rep, 2016. doi:10.1038/srep20602.

4.      Teng Fei, Yang Fang, Huang Shi, Bo Cunpei, Zhengjiang Xu,Amnon Amir, Knight Rob, Ling Junqi, Xu Jian: Prediction of Early Childhood Caries via Spatial-temporal Variation of Oral Microbiota, Cell Host &Microbe, 2015.http://dx.doi.org/10.1016/j.chom.2015.08.005.

5.      Tepper Bruce, Howard Brian, Schnell Daniel, Mills Lisa, Xu Jian, In Vitro Method for Prediction of Plaque Reduction by Dentifrice, J Microbiol. Methods, 2015. doi: 10.1016/j.mimet.2015.06.017

6.      Huang Shi, Li Rui, Zeng Xiaowei, He Tao, Zhao Helen, Chang Alice, Bo Cuipei, Chen Jie, Yang Fang, Knight Robin D., Liu Jiquan, Davis Catherine, Xu Jian: Predictive modeling of gingivitis severity and susceptibility via oral microbiota. ISME J, 2014,8, 1768–1780; doi:10.1038/ismej.2014.32.

7.      Tu Qichao, He Zhili, Li Yan, Chen Yanfei, Deng Ye, Lin Lu, Hemme Christopher, Tong Yuan, Nostrand Joy Van, Wu Liyou, Zhou Xuedong, Shi Wenyuan, Li Lanjuan, Xu Jian, Zhou Jizhong: Development of Humichip for Functional Profiling of Human Microbiomes.PLoS ONE 2014, DOI: 10.1371/journal.pone.0090546

8.      Yang Fang, Ning Kang, Chang Xingzhi, Yuan Xiao, Tu Qichao, Yuan Tong, Deng Ye, Hemme Christopher L., Van Nostrand Joy, Cui Xinping, He Zhili, Chen Zhenggang, Guo Dawei, Yu Jiangbo, Zhang Yue, Zhou Jizhong, Xu Jian: Saliva Microbiota Carry Caries-Specific Functional Gene Signatures. PLoS ONE 2014, 9(2):e76458.

9.      Yang F., Huang S., He T., Catrenich C., Teng F., Bo C., Chen J., Liu J., Li J., Song Y., Li R., Xu J.: Microbial Basis of Oral Malodor Development in Humans. J Dent Res 2013, 92(12):1106-1112.

10.  Lee Yong-Jin, Van Nostrand Joy D., Tu Qichao, Lu Zhenmei, Cheng Lei, Yuan Tong, Deng Ye, Carter Michelle Q., He Zhili, Wu Liyou, Yang Fang, Xu Jian, Zhou Jizhong: The Pathochip, a Functional Gene Array for Assessing Pathogenic Properties of Diverse Microbial Communities. ISME J 2013, 7(10):1974-1984.

11.  Yang Fang, Zeng Xiaowei, Ning Kang, Liu Kuan-Liang, Lo Chien-Chi, Wang Wei, Chen Jie, Wang Dongmei, Huang Ranran, Chang Xingzhi, Chain Patrick S., Xie Gary, Ling Junqi, Xu Jian: Saliva Microbiomes Distinguish Caries-Active from Healthy Human Populations. ISME J 2012, 6(1):1-10.

12.  Huang Shi, Yang Fang, Zeng Xiaowei, Chen Jie, Li Rui, Wen Ting, Li Chun, Wei Wei, Liu Jiquan, Chen Lan, Davis Catherine, Xu Jian: Preliminary Characterization of the Oral Microbiota of Chinese Adults with and without Gingivitis. BMC Oral Health 2011, 11(1):33.

13.  Xu Jian, Mahowald Michael A., Ley Ruth E., Lozupone Catherine A., Hamady Micah, Martens Eric C., Henrissat Bernard, Coutinho Pedro M., Minx Patrick, Latreille Philippe, Cordum Holland, Van Brunt Andrew, Kim Kyung, Fulton Robert S., Fulton Lucinda A., Clifton Sandra W., Wilson Richard K., Knight Robin D., Gordon Jeffrey I.: Evolution of Symbiotic Bacteria in the Distal Human Intestine. PLoS Biol 2007, 5(7):e156.

Selected peer commentaries: Walker A, Say hello to our little friends, Nature Reviews Microbiology, 5:572-3 (2007).

14.  Oh Jung D., Kling-Bäckhed Helene, Giannakis Marios, Xu Jian, Fulton Robert S., Fulton Lucinda A., Cordum Holland S., Wang Chunyan, Elliott Glendoria, Edwards Jennifer, Mardis Elaine R., Engstrand Lars G., Gordon Jeffrey I.: The Complete Genome Sequence of a Chronic Atrophic Gastritis Helicobacter Pylori Strain: Evolution During Disease Progression. Proc Natl Acad Sci USA 2006, 103(26):9999-10004.

15.  Chen Swaine L., Hung Chia-Seui, Xu Jian, Reigstad Christopher S., Magrini Vincent, Sabo Aniko, Blasiar Darin, Bieri Tamberlyn, Meyer Rekha R., Ozersky Philip, Armstrong Jon R., Fulton Robert S., Latreille J. Phillip, Spieth John, Hooton Thomas M., Mardis Elaine R., Hultgren Scott J., Gordon Jeffrey I.: Identification of Genes Subject to Positive Selection in Uropathogenic Strains of Escherichia Coli: A Comparative Genomics Approach. Proc Natl Acad Sci USA 2006, 103(15):5977-5982.

16.  Sonnenburg Justin L., Xu Jian, Leip Douglas D., Chen Chien-Huan, Westover Benjamin P., Weatherford Jeremy, Buhler Jeremy D., Gordon Jeffrey I.: Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont. Science 2005, 307(5717):1955-1959.

17.  Xu Jian, Chiang Herbert C., Bjursell Magnus K., Gordon Jeffrey I.: Message from a Human Gut Symbiont: Sensitivity Is a Prerequisite for Sharing. Trends Microbiol 2004, 12(1):21-28.

18.  Xu Jian, Gordon Jeffrey I.: Honor Thy Symbionts. Proc Natl Acad Sci USA 2003, 100(18):10452-10459.

19.  Xu Jian, Bjursell Magnus K., Himrod Jason, Deng Su, Carmichael Lynn K., Chiang Herbert C., Hooper Lora V., Gordon Jeffrey I.: A Genomic View of the Human-Bacteroides Thetaiotaomicron Symbiosis. Science 2003, 299(5615):2074-2076.

Selected peer-reviewed commentaries: Gilmore MS and Ferretti JJ. (2003).Microbiology. The thin line between gut commensal and pathogen. Science 299:1999-2002.  Comstock LE and Coyne MJ. (2003). Bacteroides thetaiotaomicron: a dynamic, niche-adapted human symbiont. BioEssays 10:926-9.

20.  Hooper Lora V., Xu Jian, Falk Per G., Midtvedt Tore, Gordon Jeffrey I.: A Molecular Sensor That Allows a Gut Commensal to Control Its Nutrient Foundation in a Competitive Ecosystem. Proc Natl Acad Sci USA 1999, 96(17):9833-9838.

Area II. Synthetic Biology in Microalgal CO2 conversion and Bacterial Cellulolysis

 

21.  Li Wei, Wenxu Zhou, Yandu Lu, Xiaoyan Jing, Qingtao Wang, Hanhua Hu, Qiang Hu, Jian Xu, Dissecting and engineering microalgal carbon concentrating mechanisms for industrial-CO2-activated super-production of biomass. Under review.

22.  Yi Xin, Yandu Lu, Yi-Ying Lee, Li Wei, Qingtao Wang, Jing Jia, Dongmei Wang, Qiang Hu, Jin Liu, Yantao Li, Jian Xu, Type-2Diacylglycerol Acyltransferases from three distinct ancestors collaborate to produce triacylglycerolsin the industrial microalgaNannochloropsis oceanica, under review.

23.  Li Wei, Qingtao Wang, Yi Xin, Yandu Lu, Jian Xu, Overexpression of nuclear-encoded RuBisCO activase elevates biomass productivity in industrial oleaginous microalgae, Plant Biotechnol J, Under revision.

24.  Li Wei, Yi Xin, Qintao Wang, Juan Yang,Hanhua Hu, Jian Xu, RNAi-based targeted gene-knockdown in model oleaginous microalgae Nannochloropsis spp.The Plant Journal, 2016, in press.

25.  Qintao Wang, Yandu Lu, Yi Xin, Li Wei, Shi Huang, Jian Xu, Genome editing of model oleaginous microalgae Nannochloropsis spp. by CRISPR/Cas9, The Plant Journal, 2016. DOI: 10.1111/tpj.13307.

26.  Xu Chenggang, Huang Ranran, Teng Lin, Jing Xiaoyan, Hu Jianqiang, Cui Guzheng, Wang Yilin, Cui Qiu, Xu Jian: Cellulosome stoichiometry in Clostridium cellulolyticum is regulated by selective RNA processing and stabilization. Nature Communications,2015,6:6900 doi: 10.1038/ncomms7900.

27.  Lin Teng, Kun Wang, Jian Xu, Chenggang Xu, Flavin mononucleotide (FMN)-based fluorescent protein (FbFP) as reporter for promoter screening in Clostridium cellulolyticum, J Microbiol.Methods, 2015.

28.  Bareket Dassa, Sagar Utturkar, Richard Hurt Jr., Dawn Klingeman, Martin Keller, Jian Xu, Harish Kumar Reddy, Ilya Borovok, Inna Rozman Grinberg, Raphael Lamed, Olga Zhivin, Edward Bayer, and Steven Brown,Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603,Genome Announcement, 2015

29.  Chew Yee Ngan, Chee-Hong Wong, Cindy Choi, Yuko Yoshinaga, KatherineLouie, Jing Jia, Cindy Chen, Benjamin Bowen, Lauriebeth Leonelli, Rita Kuo,Richard Baran, José G. García-Cerdán, Abhishek Pratap, Mei Wang, Joanne Lim,Hope Tice, Chris Daum, Jian Xu, Trent Northen, Axel Visel, James Bristow,Krishna K. Niyogi, Chia-Lin Wei, Lineage-Specific Chromatin Signatures Reveal a Master Lipid Switch in Microalgae, Nature Plants, 2015,doi:10.1038/nplants.2015.107.

30.  Jianhua Fan, Kang Ning,Xiaowei Zeng, Yuanchan Luo, Dongmei Wang, Jianqiang Hu, Jing Li, Hui Xu, Jianke Huang, Minxi Wan, Weiliang Wang, Daojing Zhang, Guomin Shen, Conglin Run, Junjie Liao, Lei Fang, Shi Huang, Xiaoyan Jing, Xiaoquan Su, Anhui Wang, Lili Bai, Zanmin Hu, Jian Xu and Yuanguang Li,Genomic Foundation of Starch to LipidSwitch in Oleaginous Chlorella. Plant Physiology, 2015, DOI:10.1104/pp.15.01174.

31.  Lu Yandu and Xu Jian: Phytohormones in microalgae: a new opportunity for microalgal biotechnology?Trends Plant Sci, 2015. DOI: 10.1016/j.tplants.2015.01.006 (Cover Article).

32.  Jia Jing, Han Danxiang, Gerken Henri, Li Yantao, Sommerfeld Milton, Hu Qiang, Xu Jian: Molecular mechanisms for photosynthetic carbon partitioning into storage neutral lipids in Nannochloropsis oceanica under nitrogen-depletion conditions. Algal Research2015, 7: 66-77. doi:10.1016/j.algal.2014.11.005

33.  Zhou Qian, Liu ZL Lewis, Ning Kang, Wang Anhui, Zeng Xiaowei, Xu Jian: Genomic and transcriptomic analysesreveal that MAPK- andphosphatidylinositol-signaling pathwaysmediate tolerance to5-hydroxymethyl-2-furaldehyde forindustrial yeastSaccharomycescerevisiae, Sci Rep, 2014 Oct 9;4:6556. doi: 10.1038/srep06556.

34.  Lu Yandu, Danuše Tarkowská, Veronika Turečková, Luo Tingwei, Xin Yi, Li Jing, Wang Qintao, Nianzhi Jiao, Strnad Miroslav, Xu Jian:  Antagonistic roles of abscisic acid and cytokinin during response to nitrogen depletion in oleaginous microalga Nannochloropsis oceanica expand the evolutionary breadth of phytohormone function. Plant J, 2014,DOI: 10.1111/tpj.12615.

35.  Hu Jianqiang, Wang Dongmei, Li Jing, Jing Gongchao, Ning Kang, Xu Jian: Whole-Genome Identification of Transcription Factors and Transcription-factor Binding Sites in oleaginous microalgae Nannochloropsis. Sci Rep, 2014, 4: 5454|DOI:10.1038/srep05454.

36.  Ji Yuetong, He Yuehui, Cui Yanbin, Wang Tingting, Wang Yun, Li Yuanguang, Huang Wei E, Xu Jian: Raman Spectroscopy Provides a Rapid, Non-invasive Method for Quantitation of Starch in Live, Unicellular Microalgae.Biotechnology Journal, 2014. DOI: 10.1002/biot.201400165 

37.  Wang Tingting, Ji Yuetong, Wang Yun, Li Jing, Huang Shi, Jia Jing, Han Danxiang, Hu Qiang, Huang Wei E, Xu Jian: Quantitative Dynamics of Triacylglycerol Accumulation in Microalgae Populations at Single-Cell Resolution Revealed by Raman Spectrometry. Biotech Biofuels, 2014, 7:58. DOI: 10.1186/1754-6834-7-58.

38.  Lu Yandu, Zhou Wenxu, Wei Li, Li Jing, Jia Jing, Li Fei, Smith Steven, Xu Jian: Regulation of the Cholesterol Biosynthetic Pathway and Its Integration with Fatty Acid Biosynthesis in the Oleaginous Microalga Nannochloropsis oceanica. Biotech Biofuels, 2014, 7:81. doi:10.1186/1754-6834-7-81.

39.  Li Jing, Han Danxiang, Wang Dongmei, Ning Kang, Jia Jing, Wei Li, Jing Xiaoyan, Huang Shi, Chen Jie, Li Yantao, Hu Qiang, Xu Jian: Choreography of Transcriptomes and Lipidomes ofNannochloropsis Reveals the Mechanisms of Oleaginousness in Microalgae.Plant Cell 2014. 10.1105/tpc.113.121418.

40.  Wang Dongmei, Ning Kang, Li Jing, Hu Jianqiang, Han Danxiang, Wang Hui, Zeng Xiaowei, Jing Xiaoyan, Zhou Qian, Su Xiaoquan, Chang Xingzhi, Wang Anhui, Wang Wei, Jia Jing, Wei Li, Xin Yi, Qiao Yinghe, Huang Ranran, Chen Jie, Han Bo, Yoon Kangsup, Hill Russell T., Zohar Yonathan, Chen Feng, Hu Qiang, Xu Jian: Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits. PLoS Genet 2014, 10(1):e1004094.

41.  Wei Li, Xin Yi, Wang Dongmei, Jing Xiaoyan, Zhou Qian, Su Xiaoquan, Jia Jing, Ning Kang, Chen Feng, Hu Qiang, Xu Jian: Nannochloropsis Plastid and Mitochondrial Phylogenomes Reveal Organelle Diversification Mechanism and Intragenus Phylotyping Strategy in Microalgae. BMC Genomics 2013, 14(1):534.

42.  Wang Dongmei, Lu Yandu, Huang  He, Xu Jian: Establishing Oleaginous Microalgae Research Models for Consolidated Bioprocessing of Solar Energy. Adv Biochem Eng Biotechnol 2012, 128:69-84.

43.  Xu Chenggang, Huang Ranran, Teng Lin, Wang Dongmei, Hemme Christopher, Borovok Ilya, He Qiang, Lamed Raphael, Bayer Edward, Zhou Jizhong, Xu Jian: Structure and Regulation of the Cellulose Degradome in Clostridium cellulolyticum. Biotechnol Biofuels 2013, 6(1):73.

44.  Lin Lu, Xu Jian: Dissecting and Engineering Metabolic and Regulatory Networks of Thermophilic Bacteria for Biofuel Production. Biotechnol Adv 2013, 31(6):827-837.

45.  Lin Lu, Ji Yuetong, Tu Qichao, Huang Ranran, Teng Lin, Zeng Xiaowei, Song Houhui, Wang Kun, Zhou Qian, Li Yifei, Cui Qiu, He Zhili, Zhou Jizhong, Xu Jian: Microevolution from Shock to Adaptation Revealed Strategies Improving Ethanol Tolerance and Production in Thermoanaerobacter. Biotechnol Biofuels 2013, 6(1):103.

46.  Dai Xin, Zhu Yaxin, Luo Yingfeng, Song Lei, Liu Di, Liu Li, Chen Furong, Wang Min, Li Jiabao, Zeng Xiaowei, Dong Zhiyang, Hu Songnian, Li Lingyan, Xu Jian, Huang Li, Dong Xiuzhu: Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen. PLoS ONE 2012, 7(7):e40430.

47.  Lin Lu, Song Houhui, Tu Qichao, Qin Yujia, Zhou Aifen, Liu Wenbin, He Zhili, Zhou Jizhong, Xu Jian: The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria. PLoS Genet 2011, 7(10):e1002318.

48.  Xu Chenggang, Qin Yong, Li Yudong, Ji Yuetong, Huang Jianzhong, Song Houhui, Xu Jian: Factors Influencing Cellulosome Activity in Consolidated Bioprocessing of Cellulosic Ethanol. Bioresource Technol 2010, 101(24):9560-9569.

49.  Lin Lu, Song Houhui, Ji Yuetong, He Zhili, Pu Yunting, Zhou Jizhong, Xu Jian: Ultrasound-Mediated DNA Transformation in Thermophilic Gram-Positive Anaerobes. PLoS ONE 2010, 5(9):e12582.

50.  Hemme Christopher L., Fields Matthew W., He Qiang, Deng Ye, Lin Lu, Tu Qichao, Mouttaki Housna, Zhou Aifen, Feng Xueyang, Zuo Zheng, Ramsay Bradley D., He Zhili, Wu Liyou, Van Nostrand Joy, Xu Jian, Tang Yinjie J., Wiegel Juergen, Phelps Tommy J., Zhou Jizhong: Correlation of Genomic and Physiological Traits of Thermoanaerobacter Species with Biofuel Yields. Appl Environ Microbiol 2011, 77(22):7998-8008.

51.  Mcbride Mark J., Xie Gary, Martens Eric C., Lapidus Alla, Henrissat Bernard, Rhodes Ryan G., Goltsman Eugene, Wang Wei, Xu Jian, Hunnicutt David W., Staroscik Andrew M., Hoover Timothy R., Cheng Yi-Qiang, Stein Jennifer L.: Novel Features of the Polysaccharide-Digesting Gliding Bacterium FlavobacteriumJohnsoniae as Revealed by Genome Sequence Analysis. Appl Environ Microbiol 2009, 75(21):6864-6875.

52.  Feng Xueyang, Mouttaki Housna, Lin Lu, Huang Rick, Wu Bing, Hemme Christopher L., He Zhili, Zhang Baichen, Hicks Leslie M., Xu Jian, Zhou Jizhong, Tang Yinjie: Characterization of the Central Metabolic Pathways in Thermoanaerobacter Sp. Strain X514 Via Isotopomer-Assisted Metabolite Analysis. Appl Environ Microbiol 2009, 75(15):5001-5008.

Area III. Single-Cell Raman Imaging, Raman-activated Cell Sorting and Computational Metagenomics: Instrument/Method Development and Technical Platforms

 

53.  Yun Wang, Yizhi Song, Yifan Tao, Howbeer Muhamadali, Royston Goodacre, Ning-Yi Zhou, Gail M. Preston, Jian Xu, Wei E. Huang,Reverse and multiple stable isotope probing to study bacterial metabolism and interactions at the single cell level, Anal Chem, 2016, 88(19):9443-9450.

54.  Lin Teng, Xian Wang, Xiaojun Wang, Lihui Ren, Tingting Wang, Yun Wang, Yuetong Ji, Wei E. Huang, Jian Xu, Label-free, rapid and quantitative phenotyping of stress response via Single-Cell Raman Microspectroscopy and ramanome, Sci Rep, 2016. DOI:10.1038/srep34359.

55.  Chunyu Li, Jian Xu and Bo Ma, A LEGO-like dynamic droplet-based system with advantages from both static and mobile droplet techniques, under review.

56.  Yufei Shan, Lihui Ren, Xiaonan Cui, Chunyu Li, Jian Xu and Bo Ma, Droplet-based single-cell culture coupled with smartphone imaging for portableand rapid bacteria quantification, under review.

57.  Wang Zongmin, Lu Zhenmei, Huang Shi, Zeng Xiaowei, Su Xiaoquan, Ning Kang, Xu Jian, Xu Zhenghong: Microbiota based modeling of vinegar fermentation process, under review.

58.  Ying Wang, Lijuan Su, Shi Huang, Cunpei Bo, Sen Yang, Yan Li, Fengqin Wang, Hui Xie, Jian Xu, Andong Song:Diversity and Resilience of the Wood-Feeding Higher Termite Mironasutitermes shangchengensis Gut Microbiota in response to Temporal and Diet Variations, Ecology and Evolution, 2016. DOI: 10.1002/ece3.2497

59.  Lijuan Su, Lele Yang, Shi Huang, Xiaoquan Su, Yan Li, Fengqin Wang, Wang E, Kang Ning,  Jian Xu, Andong Song, Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites, Journal of Insect Science, 2016 Sep 16;16(1). pii: 97. doi: 10.1093/jisesa/iew081.

60.  Ji Yuetong, Wang Tingting, He Yuehui, Huang Wei E., Hu Qiang, Xu Jian, Single cell and systems biology tools for biofuel production, book chapter, Hydrocarbon and Lipid Microbiology Protocols. Springer, 2016.ISBN 978-3-662-49131-7.

61.  Wang Yun, Song Yizhi, Thompson Ian P., Xu Jian, Huang Wei E., Single-cell metabolomics, book Chapter,Hydrocarbon and Lipid Microbiology Protocols. Springer, 2016.ISBN 978-3-662-49131-7.

62.  Zhang Peiran, Song Yizhi, Thompson Ian P, Ma Bo, Xu Jian, Huang Wei E., Single cell biotechnology for uncultured microorganisms, book chapter, Hydrocarbon and Lipid Microbiology Protocols. Springer, 2016.ISBN 978-3-662-49131-7.

63.  Huang Wei E., Song Yizhi, Xu Jian: Single cell biotechnology to shed a light on biological 'dark matter' in nature. Microbial Biotechnology2015, 8: 15-16.

64.  Qiang Zhang, Chunbo Mou,Peiran Zhang, Honglei Gou, Zhongyi Zhang, Wei E. Huang, Menglong Yang, Jian Xu and Bo Ma: Towards High-throughput Microfluidic Raman-activated Cell Sorting, Analyst, 2015, 140(18). DOI:10.1039/C5AN01074H.

65.  Zhang Peiran, Ren Lihui, Zhang Xu, Shan Yufei, Wang Yun, Ji Yuetong, Yin Huabin, Huang Wei E., Xu Jian, Ma Bo, Raman Activated Cell Sorting Based on Dielectrophoretic Single-cell Trap and Release, Analytical Chemistry2015, DOI: 10.1021/ac503974e.

66.  Zhang Qiang, Zhang Peiran, et al, Xu Jian, Ma Bo: On-demand control of microfluidic flow via capillary-tuned solenoid microvalve suction, Lab Chip,2014 Dec 21;14(24):4599-603. doi: 10.1039/c4lc00833b. Epub 2014 Sep 18.

67.  Li Chunyu, Xu Jian, Ma Bo: Precise quantitative addition of multiple reagents into droplets in sequence using glass fiber-induced droplet coalescence.Analyst, 2015,140, 701-705. DOI: 10.1039/C4AN01852D.

68.  Li Chunyu, Xu Jian, Ma Bo: A Self-Powered Microfluidic Monodispersed Droplet Generator with Capability of Multi-Sample Introduction. Microfluidics and Nanofluidics, 07 Oct 2014.

69.  Zhang Dayi, Berry James, Zhu Di, Jiang Bo, Wang Yun, Chen Yin, Huang Shi, Langford Harry, Li Guanghe, Xu Jian, Eric Aries and Wei E. Huang:Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community,ISME J, 2014Sep 5. doi: 10.1038/ismej.2014.161.

70.  Ren Lihui, Su Xiaoquan, Wang Yun, Xu Jian, Ning Kang: Qspec: Online Control and Data Analysis System for Single-Cell Raman Spectroscopy. Peer J, in press.

71.  Xinwei Cheng, Xiaoquan Su, Xiaohua Chen, Huanxin Zhao, Cunpei Bo, Jian Xu, Hong Bai, and Kang Ning: Biological Ingredient Analysis of Traditional Chinese Medicine Preparation based on High-throughput Sequencing: the Story for Liuwei Dihuang Wan. Sci Rep, 2014 4:5147, doi:10.1038/srep05147. 

72.  Wang Yun, Song Yizhi, Zhu Di, Ji Yuetong, Tingting Wang, Mcilvena David, Yin Huabing, Xu Jian, Huang Wei E: Probing and Sorting Single Cells—the Application of a Raman-Activated Cell Sorter. Spectroscopy Europe 2013, 25:5.

73.  Wang Yun, Ji Yuetong, Wharfe Emma S., Meadows Roger S., March Peter, Goodacre Royston, Xu Jian, Huang Wei E.: Raman Activated Cell Ejection for Isolation of Single Cells. Anal Chem 2013, 85(22):10697-10701.

74.  Zhou Qian, Su Xiaoquan, Wang Anhui, Xu Jian, Ning Kang: QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data. PLoS ONE 2013, 8(4):e60234.

75.  Li Mengqiu, Xu Jian, Romero-Gonzalez Maria, Banwart Steve A., Huang Wei E.: Single Cell Raman Spectroscopy for Cell Sorting and Imaging. Curr Opin Biotechnol 2012, 23(1):56-63.

76.  You Na, Murillo Gabriel, Su Xiaoquan, Zeng Xiaowei, Xu Jian, Ning Kang, Zhang Shoudong, Zhu Jiankang, Cui Xinping: SNP Calling Using Genotype Model Selection on High-Throughput Sequencing Data. Bioinformatics 2012, 28(5):643-650.

77.  Xu Meiying, Chen Xingjuan, Qiu Mengde, Zeng Xiaowei, Xu Jian, Deng Daiyong, Sun Guoping, Li Xiang, Guo Jun: Bar-Coded Pyrosequencing Reveals the Responses of Pbde-Degrading Microbial Communities to Electron Donor Amendments. PLoS ONE 2012, 7(1):e30439.

78.  Wang Yun, Chen Yin, Zhou Qian, Huang Shi, Ning Kang, Xu Jian, Kalin Robert M., Rolfe Stephen, Huang Wei E.: A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community. PLoS ONE 2012, 7(10):e47530.

79.  Wang Bao-Zhan, Zhang Cai-Xia, Liu Ji-Liang, Zeng Xiao-Wei, Li Feng-Rui, Wu Yu-Cheng, Lin Xian-Gui, Xiong Zheng-Qin, Xu Jian, Jia Zhong-Jun: Microbial Community Changes Along a Land-Use Gradient of Desert Soil Origin. Pedosphere 2012, 22(5):593-603.

80.  Su Xiaoquan, Xu Jian, Ning Kang: Meta-Storms: Efficient Search for Similar Microbial Communities Based on a Novel Indexing Scheme and Similarity Score for Metagenomic Data. Bioinformatics 2012, 28(19):2493-2501.

81.  Su Xiaoquan, Xu Jian, Ning Kang: Parallel-Meta: Efficient Metagenomic Data Analysis Based on High-Performance Computation. BMC Syst Biol 2012, 6(Suppl 1):S16.

82.  Jian Xiao-Hong, Pan Hai-Xue, Ning Ting-Ting, Shi Yuan-Yuan, Chen Yong-Sheng, Li Yan, Zeng Xiao-Wei, Xu Jian, Tang Gong-Li: Analysis of Ym-216391 Biosynthetic Gene Cluster and Improvement of the Cyclopeptide Production in a Heterologous Host. ACS Chem Biol 2012, 7(4):646-651.

83.  Xia Weiwei, Zhang Caixia, Zeng Xiaowei, Feng Youzhi, Weng Jiahua, Lin Xiangui, Zhu Jianguo, Xiong Zhengqin, Xu Jian, Cai Zucong, Jia Zhongjun: Autotrophic Growth of Nitrifying Community in an Agricultural Soil. ISME J 2011, 5(7):1226-1236.

84.  Su Xiaoquan, Xu Jian, Ning Kang: Parallel-Meta: A High-Performance Computational Pipeline for Metagenomic Data Analysis. In: Systems Biology (ISB), 2011 IEEE International Conference on: 2-4 Sept. 2011 2011. 173-178.

85.  Su Xiaoquan, Ma Yongzheng, Yang Hongwei, Chang Xingzhi, Nan Kai, Xu Jian, Ning Kang: An Open-Source Collaboration Environment for Metagenomics Research. In: Proceedings of the 2011 IEEE Seventh International Conference on eScience. 2116560: IEEE Computer Society 2011: 7-14.

86.  Xu Jian, Gordon Jeffrey I.: Maplinker: A Software Tool That Aids Physical Map-Linked Whole Genome Shotgun Assembly. Bioinformatics 2005, 21(7):1265-1266.

87.  Mitreva Makedonka, Mccarter James, Arasu Prema, Hawdon John, Martin John, Dante Mike, Wylie Todd, Xu Jian, Stajich Jason, Kapulkin Wadim, Clifton Sandra, Waterston Robert, Wilson Richard: Investigating Hookworm Genomes by Comparative Analysis of Two Ancylostoma Species. BMC Genomics 2005, 6(1):58.

88.  Ippolito Joseph E., Xu Jian, Jain Sanjay, Moulder Krista, Mennerick Steven, Crowley Jan R., Townsend R. Reid, Gordon Jeffrey I.: An Integrated Functional Genomics and Metabolomics Approach for Defining Poor Prognosis in Human Neuroendocrine Cancers. Proc Natl Acad Sci USA 2005, 102(28):9901-9906.

89.  Magrini Vincent, Warren Wesley C., Wallis John, Goldman William E., Xu Jian, Mardis Elaine R., Mcpherson John D.: Fosmid-based Physical Mapping of the Histoplasma capsulatum Genome. Genome Res 2004, 14(8):1603-1609.


Research Interests

single-cell analysis, scientific instrument development, ocean carbon cycling, microalgal biofuels, cellulosic biofuels, human microbiota

Invited Talks

  1. Genetic Foundations of Robust Oil Production in Microalgae - new generation genomics technologies for algal feedstock development. 3rd Algae World Asia conference, Singapore, Oct 19-20, 2010
  2. The genomics of fuel producing microalgae. 9th International Marine Biotechnology Conference, Qingdao, Oct 8-12, 2010
  3. Genetic Foundations of Robust Oil Production in Microalgae, Algae Biomass Summit, Phoenix, AZ, Sept 28-30, 2010
  4. New-generation metagenomics approaches. Second-generation Sequencing Workshop (sponsored by NIH-USA), Shanghai, July 26-30, 2010 
  5. Dissecting the structure and function of complex microbial communities using the new-generation metagenomics approach. The 4th Industrial Biotechnology Summit of China, Huzhou, Apr 26-29, 2010
  6. Establishment of a novel Nannochloropsis-based research model and platform technology for algal biofuel production. Innovation Seminar Series, Institute of Hydrobiology, Chinese Academy of Sciences, May 31, 2010
  7. New-generation genomics and transcriptomics approaches in algal biofuel development. Bioscience Division, Los Alamos National Laboratory, Los Alamos, NW, April 20, 2010
  8. The promises and risks of Synthetic Biology in algal-biofuel development, Risk Governance of Synthetic Biology, International Risk Governance Council, Geneva, Switzerland, Oct 26-27, 2009
  9. New-generation genomics and transcriptomics approaches in algal biofuel development, US-China BioEnergy Conference and US-China Forum on A Sustainable Future through Bioenergy and Biomass Usage, Beijing, Oct 23-25, 2009
  10. New-generation genomics approaches in biofuel development, Sino-Denmark Joint Research Center Symposium, Beijing, Oct 19-21, 2009
  11.  Development of novel microalgae for robust biofuel production, Department of Mechanical Engineering, Colorado State University, Fort Collins, Oct 16, 2009 
  12. New-generation genomics approaches in biofuel development, EMBO World Practical Course: Computational Biology: from (meta)genomes to phenotype and environment, Shanghai, Aug 16-22, 2009
  13. The application of genomic approaches in developing new-generation biofuels, Department of Plant Biology and Department of Civil and Environmental Engineering, Arizona State University, Tempe, Arizona, Apr 2, 2009
  14. Genomic approaches in developing reconstructed microbial communities for biofuel development, Department of Botany and Microbiology, University of Oklahoma, Oklahoma City, Oklahoma, March 28, 2009
  15. High-performance computing in bioenergy research and development, Sino-US Symposium on High-performance Computing, Beijing, Dec 12, 2008
  16. Genomic approaches in developing thermophilic Clostridia for production of cellulosic ethanol, McDonnell International Scholars Academy 2nd International Symposium of Energy and Environment, Hong Kong, Dec 08-11, 2008
  17. Genomics approaches in dissecting complex microbial communities in bioenergy conversion, Sino-USA BioEnergy Forum and the Joint Annual Conference of American Society of Microbiology and Chinese Society of Microbiology, Haikou, Nov 8, 2008
  18. New-Generation Biofuel Research and Development in Chinese Academy of Sciences, Synthetic Biology 4.0, Hong Kong, Oct 10-12, 2008 
  19.  Genomics approaches in dissecting complex microbial communities in bioenergy conversion, 4th SCOPE Workshop on Microbial Environmental Genomics, Changsha, Sept 20, 2008
  20. Genomic Approaches in exploring bioenergy microbial communities. 454 Life Science, Branford, CT, USA，June 9, 2008
  21. BioEnergy Initiatives in Chinese Academy of Sciences, Monsanto Inc, St Louis, MO, USA. Apr 23, 2008
  22. Characterization and exploitation of natural complex microbial communities for bioenergy applications. The 2nd Industrial Biotechnology Summit of China, Tianjin, Apr 17-19, 2008

Main Projects

Ministry of Science and Technology of China 
Analysis of genome-wide networks and design of functional modules. 973 Program, 2012-2016, Co-PI
Key technology and application of solid-state fermentation with straw to produce ethanol. National Key Technology Support Program, 2011-2013, Co-PI 
Development of high-throughput single cell screening method by Raman clamp. Special Foundation for Innovative Approach, 2011-2012, PI
Development of designer cellulosome systems in Clostridia for enhanced cellulosic biomass conversion. China-Israel Research Collaboration, 2010-2012, PI on Chinese side (PI on Israel side: Ed Bayer of Weizmann Institute of Science) 
Algorithm and tool development for analyzing metagenome data produced by second-generation DNA sequencers. 863 Program, 2009-2011, Co-PI 
Natural Science Foundation of China
Establishment of a novel Nannochloropsis-based research model and platform technology for algal biofuel production. Major International Cooperation Program, 2011-2013, PI 
Uncovering the genetic factors underlying ethanol tolerance in ethanogenic thermophile Thermoanaerobacter. General Program, 2009-2011, PI
Chinese Academy of Sciences
Microalgal energy and biorefinery. International Partnership for Innovation Program, 2010-2012, PI
The diversity and molecular mechanism of bacterial degradation of cellulose. Hundred Talent Award Program, 2008-2011, PI
Construction of a genetic manipulation system for Clostridia and Thermoanaerobacter. Knowledge Innovation Program, 2008-2011, PI
Discovery and mining of oil-producing algae through high-throughput genomics approaches. Special Foundation, 2009-2010, PI
An E-Science Environment for the integrated analysis of the new-generation metagenomes of microbial communities. Foundation for Information Technology, 2009-2010, PI 
Shandong Province
A systems biology approach in understanding cellulolytic and ethanogenic Clostridia. Outstanding Young Investigator Award of Shandong, 2008-2011, PI

Students

已指导学生

林璐  博士研究生  071010-生物化学与分子生物学  

李敬  博士研究生  071010-生物化学与分子生物学  

黄冉冉  博士研究生  071010-生物化学与分子生物学  

魏力  博士研究生  071010-生物化学与分子生物学  

辛一  博士研究生  071010-生物化学与分子生物学  

加晶  博士研究生  071010-生物化学与分子生物学  

何曰辉  硕士研究生  085238-生物工程  

滕琳  博士研究生  071010-生物化学与分子生物学  

黄适  博士研究生  071010-生物化学与分子生物学  

胡建强  硕士研究生  071010-生物化学与分子生物学  

王勤涛  博士研究生  071010-生物化学与分子生物学  

王险  硕士研究生  081703-生物化工  

张鹏  博士研究生  071010-生物化学与分子生物学  

荆晓艳  博士研究生  071010-生物化学与分子生物学  

何曰辉  博士研究生  071010-生物化学与分子生物学  

孙政  博士研究生  071010-生物化学与分子生物学  

苏晓泉  博士研究生  071005-微生物学  

佘依婷  硕士研究生  085238-生物工程  

现指导学生

梁文思  博士研究生  071005-微生物学  

陈荣泽  博士研究生  071005-微生物学  

徐腾  博士研究生  071005-微生物学  

李贞  硕士研究生  085238-生物工程  

王建美  博士研究生  071005-微生物学