陈 非

中国科学院北京基因组研究所

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  • 陈 非
  • 博士生导师
  • 研究员

陈 非 ( Chen Fei )

职 称: 研究员
职 务: 博士生导师
E-Mail: chenfei@big.ac.cn
学科类别: 基因组与生物信息学/合成生物学
学习经历:
1992 - 1996 四川大学生物工程系,学士学位 1997 - 2000 吉林大学材料学院,硕士学位 2000 - 2003 吉林大学 生命科学院分子酶学工程教育部重点实验室,博士学位
工作经历:

2001 - 2003 吉林大学生命科学院分子酶学工程教育部重点实验室, 助教. 2003 - 2005 吉林大学生命科学院分子酶学工程教育部重点实验室, 讲师. 2005 - 2006 美国佛罗里达大学, 博士后 2006 - 2009 美国应用分子进化研究基金会 (Foundation for Applied Molecular Evolution, FfAME), 研究员 (Research Scientist) 2009 - 2012 美国应用分子进化研究基金会 (FfAME), 高级研究员 (Senior Scientist) 2011至今 中国科学院北京基因组研究所 研究员 博士生导师

主要研究领域:

1、重大疾病精准基因组学研究:重点针对呼吸道疾病实际临床问题,应用多组学(基因组、转录组、蛋白组、代谢组、表观组等)研究手段,集成机器学习原理和数学统计模型,由面至点,致力于发现重大疾病临床诊治靶标,实现重大疾病检测窗口前移和精准治疗,切实解决一些实际临床问题。 (1)呼吸系统致病微生物基因组学研究:针对两种具有极其重要临床地位的呼吸道疾病的致病微生物——结核分枝杆菌和肺炎克雷伯菌,通过多组学数据挖掘、整合,系统解析上述致病菌的各种致病表型与基因型的关联,为结核、肺炎等呼吸道感染性疾病的精准诊治提供新靶标。 (2)宏基因组研究:以II型糖尿病、帕金森病等患者为研究对象,通过大样本量的口腔、肠道微生物宏基因组测序,完整解析患者口腔、肠道微生物特征菌群、群落结构、代谢通路等,并进行其疾病关联性分析,发现可用于诊治的特征菌和分子靶标,探索别样的惠民健康发展之路。 (3)新型结核疫苗的人工合成:通过泛基因组解析获取结核分枝杆菌复合群菌株的核心基因,整合已知必需基因而获得最小基因组;通过多组学数据的深入整合、挖掘,获取疫苗功能基因和相关调控元件,完成新型人工结核疫苗的设计、合成与评价。 2、DNA存储技术研究: DNA存储技术是一种新兴的大数据存储技术。其突破了传统以固体介质(硬盘、光盘、磁带等)为媒介的存储方式,将数据信息存储于DNA(脱氧核糖核酸)的核苷酸编码序列(A、T、C、G组合)中。相比于传统的信息存储方式,DNA存储技术具有数据密度高、保存时间长、设备能耗低、便于携带、运输等优点。我们目前正致力于开发实现上述目标的新型DNA存储技术。 本实验室挚诚欢迎各种学科背景的有为青年报考,包括但并不限于生物、医学、数学,统计,计算机等。

承担科研项目情况:

1. 国家自然科学基金面上项目:基于Hi-C及ChIA-PET技术的结核分枝杆菌复合群(MTBC)3D、4D基因组差异研究;2018 - 2021;在研,项目负责人; 2. 国家重点研发计划传染病重大专项项目:菌阴结核病与非结核分枝杆菌病鉴别诊断的创新技术研发与应用研究;2018 - 2020;在研,课题骨干; 3. 青海省科技厅重点研发与转化项目:青海牦牛基因组重测序及其肠道菌群测序分析;2017 - 2020;在研,课题负责人; 4. 科技创新特区项目:DNA存储技术研究;2018 - 2019;在研,项目负责人; 5. 中国科学院重点部署项目:建立基于宏基因组的涉毒人群推断的分析体系;2016 -2018;在研,课题负责人; 6. 国家自然科学基金面上项目:'ATCGZP'六核酸分子合成生命遗传系统的设计与构建;2015 - 2018;结题,项目负责人; 7. 国家高技术研究发展计划(863)基于微流控芯片技术的肺癌单细胞分选及基因组测序分析;2015 – 2017;结题,课题骨干; 8. 科技部重大科学基础研究项目(973):调控核酸表观遗传修饰的关键因子的发现与作用机制研究;2014 - 2018;结题,课题负责人; 9. 科技部传染病重大专项:基于二代测序技术和生物信息学的病原微生物综合分析平台,2013-2015,结题,项目骨干; 10. 中国科学院重点部署项目:基于修饰核苷酸的耐药结核杆菌检测新技术研究,2013-2015,结题,项目骨干。

代表论著:

1.Hairong Huang, Nan Ding, Tingting Yang, Cuidan Li, Xinmiao Jia, Guirong Wang, Jun Zhong, Ju Zhang, Guanglu Jiang, Shuqi Wang, Zhaojing Zong, Wei Jing, Yongliang Zhao, Shaofa Xu*, Fei Chen*. Cross-sectional whole-genome sequencing and epidemiological study of multidrugresistant Mycobacterium tuberculosis in China. Clin Infect Dis (CID), doi:10.1093/cid/ciy883, 2019.

2.Dingxia Shen, Guannan Ma, Cuidan Li, Xinmiao Jia, Chuan Qin, Tingting Yang, Lifeng Wang, Nan Ding, Liya Yue, Zhe Yin, Lijun Zeng, Yongliang Zhao, Dongsheng Zhou*, Fei Chen*. Emergence of a multidrug-resistant hypervirulent Klebsiella pneumoniae of ST23 with a rare blaCTX-M-24-harboring virulence plasmid. Antimicrob Agents Chemother (AAC), 63(3): e02273-18, 2019.

3.Ju Zhang, Xiuli Zhang, Cuidan Li, Liya Yue, Nan Ding, Tim Riordan, Li Yang, Yang Li, Charles Jen, Sen Lin, Dongsheng Zhou, Fei Chen*. Circular RNA profiling provides insights into their subcellular distribution and molecular characteristics in HepG2 cells. RNA Biology, 10.1080/15476286.2019.1565284, 2019.

4.Tingting Yang, Jun Zhong, Ju Zhang, Cuidan Li, Xia Yu, Jingfa Xiao, Xinmiao Jia, Nan Ding, Guannan Ma, Guirong Wang, Liya Yue, Qian Liang, Yongjie Sheng, Yanhong Sun, Hairong Huang* and Fei Chen*. Pan-genomic study of Mycobacterium tuberculosis reflecting the primary/secondary genes, generality/individuality, and the interconversion through copy number variations. Front Microbiol, 9: 1886, 2018.

5.Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You, Xinmiao Jia, Junhui Yang, Lingping Wang, Jinyue Wang, Haohuan Fu, Yu Kang, Fei Chen, Jun Yu, Jiayan Wu* and Jingfa Xiao*. PGAP-X: extension on pan-genome analysis pipeline. BMC Genomics, 19 (Suppl 1): 36, 2018.

6.Xinmiao Jia, Li Yang, Mengxing Dong, Suting Chen, Lingna Lv, Dandan Cao, Jing Fu, Tingting Yang, Ju Zhang, Xiangli Zhang, Yuanyuan Shang, Guirong Wang, Yongjie Sheng, Hairong Huang* and Fei Chen*. The Bioinformatics Analysis of Comparative Genomics of Mycobacterium tuberculosis Complex (MTBC) Provides Insight into Dissimilarities between Intraspecific Groups Differing in Host Association, Virulence, and Epitope Diversity. Front Cell Infect Microbiol, 7: 88, 2017.

7.Lingna Lv, Cuidan Li, Xiuli Zhang, Nan Ding, Tianshu Cao, Xinmiao Jia, Jinghui Wang, Liping Pan , Hongyan Jia, Zihui Li, Ju Zhang, Fei Chen* and Zongde Zhang*. RNA Profiling Analysis of the Serum Exosomes Derived from Patients with Active and Latent Mycobacterium tuberculosis Infection. Front Microbiol, 8: 1051, 2017.

8.Lei Zhang, Jun Zhong, Hao Liu, Kaiyun Xin, Chaoqiong Chen, Qiqi Li, Yahong Wei, Yao Wang, Fei Chen*, Xihui Shen*. Complete genome sequence of the drought resistance-promoting endophyte Klebsiella sp. LTGPAF-6F. J Biotechnol, 246: 36-39, 2017.

9.Yahong Wei , Jing Fu, Jianying Wu, Xinmiao Jia, Yunheng Zhou, Cuidan Li, Mengxing Dong, Shanshan Wang, Ju Zhang*, Fei Chen*. Bioinformatics analysis and characterization of highly efficient polyvinyl alcohol (PVA)-degrading enzymes from the novel PVA degrader Stenotrophomonas rhizophila QL-P4. Appl Environ Microbiol, 84 (1): e01898-17, 2017.

10.Qing Liu, Guocheng Liu, Ting Wang, Jing Fu, Rujiao Li, Linlin Song, Zhen-Gang Wang*, Baoquan Ding* and Fei Chen*. Enhanced Stability of DNA Nanostructures by Incorporation of Unnatural Base Pairs (UBPs). ChemPhysChem, 18(21): 2977-2980, 2017.

11.Fei Chen*, Yuan Zhang, Ashley B. Daugherty, Zunyi Yang, Ryan Shaw, Mengxing Dong, Steven A. Benner*. Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant. PLoS ONE, 12 (3), e0174163, 2017.

12.Mariko F. Matsuura, Christian B. Winiger, Ryan W. Shaw, Myong-Jung Kim, Myong-Sang Kim, Ashley B. Daugherty, Fei Chen, Patricia Moussatche, Jennifer D. Moses, Stefan Lutz, and Steven A. Benner*. A Single Deoxynucleoside Kinase Variant from Drosophila melanogaster Synthesizes Monophosphates of Nucleosides That Are Components of an Expanded Genetic System. ACS Synth Biol, 6 (3): 388 - 394, 2017.

13.Jun Yang, Yan Liu, Bing Wang, Hongzhen Lan, Ying Liu, Fei Chen, Ju Zhang and Jian Luo*. Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939. BMC Mol Biol, 18: 23, 2017.

14.Lingxiang Zhu, Jun Zhong, Xinmiao Jia, Guan Liu, Yu Kang, Mengxing Dong, Xiuli Zhang, Qian Li, Liya Yue, Cuidan Li, Jing Fu, Jingfa Xiao, Jiangwei Yan, Bing Zhang, Meng Lei, Suting Chen, Lingna Lv, Baoli Zhu, Hairong Huang* and Fei Chen*. Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio Single-Molecule Real-Time (SMRT) Technology. Nucleic Acids Res, 44(2): 730-743, 2016.

15.Xinpeng Tian, Zhewen Zhang, Tingting Yang, Meili Chen, Jie Li, Fei Chen, Jin Yang, Wenjie Li, Bing Zhang, Zhang Zhang, Jiayan Wu, Changsheng Zhang, Lijuan Long* and Jingfa Xiao*. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Front Microbiol, 7: 998, 2016.

16.Zhang Z*, Hu S*, He H*, Zhang H*, Zhang Z, Hu S, He H, Chen F, Zhao W, Xiao J, Chen LL, Xue Y, Wang X, Xia L, Wang X, Luo Y, Wu S, Hao L, Zou D, Yang L, Huang D, Xu X, Yan W, Li Q, Zhong J, Hao L, Zou D, Xu X, Huang D, Xu X, Yuan F, Zhang Y, Sang J, Ma L, Liu S, Zou D, Cheng H, Wang Y, Deng W, Zhang Z, Hu S, He H, Chen F, Chen LL, Xue Y, Ji Z. IC4R Project Consortium, Information Commons for Rice (IC4R). Nucleic Acids Res, 44 (D1): D1172-80, 2016.

17.Yu Kang, Chaohao Gu, Lina Yuan, Yue Wang, Yanmin Zhu, Xinna Li, Qibin Luo, Jingfa Xiao, Daquan Jiang, Minping Qian, Aftab Ahmed Khan, Fei Chen, Zhang Zhang*, Jun Yu*. Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks. mBio, 5(6): e01867-14, 2015.

18.Yiyangzi Ma, Na Shi, Mengtao Li, Fei Chen, Haitao Niu*. Applications of Next-generation Sequencing in Systemic Autoimmune Diseases. Genomics Proteomics Bioinformatics, 13(4):242-9, 2015.

19.Dai L, Xu C, Tian M, Sang J, Zou D, Li A, Liu G, Chen F, Wu J, Xiao J, Wang X, Yu J, Zhang Z. Community intelligence in knowledge curation: an application to managing scientific nomenclature. PLoS ONE. 8(2): e56961, 2013.

20.Yang Z, Durante M, Glushakova LG, Sharma N, Leal NA, Bradley KM, Chen F, Benner SA. Conversion strategy using an expanded genetic alphabet to assay nucleic acids. Anal Chem. 85 (9): 4705-12, 2013.

21.Fei Chen*, Mengxing Dong, Meng Ge, Lingxiang Zhu, Lufeng Ren, Guocheng Liu, and Rong Mu. The history and advances of reversible terminators used in new generations of sequencing technology. Genomics Proteomics Bioinformatics, 11(1):34-40, 2013.

22.Yang, ZY#., Chen, F.#, Brian, JA., Benner, SA. Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System. (2011) J Am Chem Soc. 133(38), 15105-12. (#Co-First Author).

23.Chen, F., Yang ZY, Yan MC, Brian JA, Wang GG, Benner SA. Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. (2011) Nucleic Acid Res. 39 (9), 3949-61.

24.Chen, F., Gaucher, E. A., Leal, N. A., Hutter, D., Havemann, S. A., Govindarajan, S., Ortlund, E. A., Benner, S. A. (2010) Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection. Proc. Natl. Acad. Sci. USA. 107, 1948-1953.

25.Yang, Z., Chen, F., Chamberlin, S. G., Benner, S. A. (2010) Expanded genetic alphabets in the polymerase chain reaction. Angew. Chem. Int. Edit, 49, 177-180. ('Faculty of 1000 Biology' Selection).

26.Hoshika, S., Chen, F., Leal, N., Benner, S.A. (2010) Artificial genetic systems. Self-avoiding DNA in PCR and multiplexed PCR. Angew. Chem. Int. Edit, 49, 5554-5557 ('Hot paper' Selection).

27.Benner, S. A., Chen, F., Yang, Z. Y. (2011) Synthetic Biology, Tinkering Biology, and Artificial Biology: A Perspective from Chemistry. pp. 69-106. In Luisi, P. L., ed. Chemical Synthetic Biology, Cambridge University pp. 69 - 106.

28.Chen, F., Li, Z., Yang, S., Wang, RJ., Liu, B., Song, YM., Sun, YH., Hao, DY. and Wang, XP. Inhibition of Ampicillin-resistance in bacteria by modified DNAzymes. (2008) Chem Res. Chinese U. 24(4), 491-5.

29.Chen, F., Wang, R., Li, Z, Liu, B., Wang, XP., Sun, YH., Hao, DY., and Zhang, J. A novel replicating circular DNAzyme. (2004) Nucleic Acid Res, 32(8), 2336-2341.

30.Chen, F., Li, Z., Wang, R.J., Liu, B., Zeng, Z., Zhang, H.Y., Zhang, J. Inhibition of Ampicillin-resistant bacteria by novel mono- and di-DNAzymes targeted to β-lactamase mRNA. (2004) Oligonucleotides, 14(2), 80-89.

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