合成生物前沿技术的开发，包括自动生物“智造”、全基因水平编辑、高通量质谱筛选等，用于燃料、药物、精细化工品等重要分子的研究与生产

   

071010-生物化学与分子生物学
071005-微生物学

合成生物学
合成生物学

2009-08--2014-12   美国伊利诺伊大学香槟分校   博士研究生
2005-09--2009-07   清华大学   学士

博士研究生

博士

2014年09月至2019年01月，伊利诺大学香槟分校，博士后

2019-04~现在, 中国科学院深圳先进技术研究院, 研究员
2014-09~2019-04,美国伊利诺伊大学基因组生物学研究所, 博士后

合成生物学

   

（1） 百特青年研究者奖, 一等奖, 其他, 2017
（2） 国家优秀自费留学生, 一等奖, 部委级, 2015

[1] 张嵩亚, 司同, 刘涛, 朱静, 陈红, 张振坤. 一种生产抗菌活性化合物的链霉菌及其分离方法和应用. CN: CN111778172A, 2020-10-16.

   

[1] Zhang, XianEn, Liu, Chenli, Dai, Junbiao, Yuan, Yingjin, Gao, Caixia, Feng, Yan, Wu, Bian, Wei, Ping, You, Chun, Wang, Xiaowo, Si, Tong. Enabling technology and core theory of synthetic biology. SCIENCE CHINA-LIFE SCIENCES. 2023, 1-44, http://dx.doi.org/10.1007/s11427-022-2214-2.
[2] Lihao Fu, Erpeng Guo, Jianzhi Zhang, Keyi Li, Yongcan Chen, Tong Si. Towards one sample per second for mass spectrometric screening of engineered microbial strains. CURRENT OPINION IN BIOTECHNOLOGY[J]. 2022, 76: [3] Songya Zhang, Jing Zhu, Shuai Fan, Wenhao Xie, Zhaoyong Yang, Tong Si. Directed evolution of a cyclodipeptide synthase with new activities via label-free mass spectrometric screening. Chemical Science[J]. 2022, https://pubs.rsc.org/en/content/articlelanding/2022/SC/D2SC01637K.
[4] Hu, Ruyun, Fu, Lihao, Chen, Yongcan, Chen, Junyu, Qiao, Yu, Si, Tong. Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments. BRIEFINGS IN BIOINFORMATICS. 2022, [5] Zhang, Yingying, Hong, Zhilai, Zhou, Liang, Zhang, Zhenkun, Tang, Ting, Guo, Erpeng, Zheng, Jie, Wang, Ciji, Dai, Lei, Si, Tong, Wang, Huan. Biosynthesis of Gut-Microbiota-Derived Lantibiotics Reveals a Subgroup of S8 Family Proteases for Class III Leader Removal. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION[J]. 2022, 61(6): http://dx.doi.org/10.1002/anie.202114414.
[6] Zhang, Jianzhi, Li, Tuo, Hong, Zhilai, Ma, Chenfei, Fang, Xiaoting, Zheng, Fengfeng, Teng, Wenkai, Zhang, Chuanlun, Si, Tong. Biosynthesis of Hybrid Neutral Lipids with Archaeal and Eukaryotic Characteristics in Engineered Saccharomyces cerevisiae. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 2022, http://dx.doi.org/10.1002/anie.202214344.
[7] Guo, Erpeng, Fu, Lihao, Fang, Xiaoting, Xie, Wenhao, Li, Keyi, Zhang, Zhiyu, Hong, Zhilai, Si, Tong. Robotic Construction and Screening of Lanthipeptide Variant Libraries in Escherichia coli. ACS SYNTHETIC BIOLOGY[J]. 2022, 11(12): 3900-3911, http://dx.doi.org/10.1021/acssynbio.2c00344.
[8] 唐婷, 付立豪, 郭二鹏, 张振坤, 王子宁, 马辰飞, 张智彧, 张建志, 黄建东, 司同. 自动化合成生物技术与工程化设施平台. 科学通报[J]. 2021, 66(3): 300-309, http://lib.cqvip.com/Qikan/Article/Detail?id=7104239788.
[9] Chen, Yongcan, Liang, Jun, Chen, Zhicong, Wang, Bo, Si, Tong. Genome-Scale Screening and Combinatorial Optimization of Gene Overexpression Targets to Improve Cadmium Tolerance in Saccharomyces cerevisiae. FRONTIERS IN MICROBIOLOGY[J]. 2021, 12: http://dx.doi.org/10.3389/fmicb.2021.662512.
[10] Zhang, Songya, Zhang, Lingxiao, Zhu, Jing, Chen, Hong, Chen, Zhicong, Si, Tong, Liu, Tao. Genomic and Metabolomic Investigation of a Rhizosphere Isolate Streptomyces netropsis WLXQSS-4 Associated with a Traditional Chinese Medicine. MOLECULES[J]. 2021, 26(8): http://dx.doi.org/10.3390/molecules26082147.
[11] 郭二鹏, 张建志, 司同. 羊毛硫肽的高通量工程改造方法新进展. 中国生物工程杂志[J]. 2021, 41(1): 30-41, http://lib.cqvip.com/Qikan/Article/Detail?id=7104036965.
[12] 胡如云, 张嵩亚, 蒙海林, 余函, 张建志, 罗小舟, 司同, 刘陈立, 乔宇. 面向合成生物学的机器学习方法及应用. 科学通报[J]. 2021, 66(3): 284-299, https://www.sciengine.com/doi/10.1360/TB-2020-0456.
[13] Tang, Ting, Fu, Lihao, Guo, Erpeng, Zhang, Zhenkun, Wang, Zining, Ma, Chenfei, Zhang, Zhiyu, Zhang, Jianzhi, Huang, Jiandong, Si, Tong. Automation in synthetic biology using biological foundries. CHINESE SCIENCE BULLETIN-CHINESE[J]. 2021, 66(3): 300-309, [14] Hu, Ruyun, Zhang, Songya, Meng, Hailin, Yu, Han, Zhang, Jianzhi, Luo, Xiaozhou, Si, Tong, Liu, Chenli, Qiao, Yu. Machine learning for synthetic biology: Methods and applications. CHINESE SCIENCE BULLETIN-CHINESE[J]. 2021, 66(3): 284-299, [15] Ren, Xiaoning, Yin, Panqing, Liang, Jun, Liu, Xiangjian, Zhan, Wugen, Niu, Jiaojiao, Si, Tong, Yu, Tao, Wu, Dan, Wang, Bo. Insight into the tannic acid-based modular-assembly strategy based on inorganic-biological hybrid systems: a material suitability, loading effect, and biocompatibility study. MATERIALS CHEMISTRY FRONTIERS[J]. 2021, 5(10): 3867-3876, http://dx.doi.org/10.1039/d0qm00887g.
[16] Zhang, Jianzhi, Chen, Yongcan, Fu, Lihao, Guo, Erpeng, Wang, Bo, Dai, Lei, Si, Tong. Accelerating strain engineering in biofuel research via build and test automation of synthetic biology. CURRENT OPINION IN BIOTECHNOLOGYnull. 2021, 67: 88-98, http://dx.doi.org/10.1016/j.copbio.2021.01.010.
[17] Xue, Pu, Si, Tong, Mishra, Shekhar, Zhang, Linzixuan, Choe, Kisurb, Sweedler, Jonathan V, Zhao, Huimin. A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids. BIOTECHNOLOGY AND BIOENGINEERING[J]. 2020, 117(7): 2131-2138, http://dx.doi.org/10.1002/bit.27343.
[18] Jiang, Shuangying, Si, Tong, Dai, Junbiao. Whole-Genome Regulation for Yeast Metabolic Engineering. SMALL METHODSnull. 2020, 4(2): https://www.webofscience.com/wos/woscc/full-record/WOS:000496824800001.
[19] 张建志, 付立豪, 唐婷, 张嵩亚, 朱静, 李拓, 王子宁, 司同. 基于合成生物学策略的酶蛋白元件规模化挖掘. 合成生物学[J]. 2020, 1(3): 319-336, http://lib.cqvip.com/Qikan/Article/Detail?id=7102848985.
[20] Lihao Fu, Jianzhi Zhang, Tong Si. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. BMC ENERGY[J]. 2020, 2(1): 1-9, http://dx.doi.org/10.1186/s42500-020-0011-8.
[21] Tan, Yang, Shen, Juntao, Si, Tong, Ho, Chun Loong, Li, Yinqing, Dai, Lei. Engineered Live Biotherapeutics: Progress and Challenges. BIOTECHNOLOGY JOURNALnull. 2020, 15(10): https://www.webofscience.com/wos/woscc/full-record/WOS:000568728800001.
[22] Chen, Yongcan, Guo, Erpeng, Zhang, Jianzhi, Si, Tong. Advances in RNAi-Assisted Strain Engineering inSaccharomyces cerevisiae. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY[J]. 2020, 8: https://doaj.org/article/5ef85bc3bad145a49fcc0d1c1f9363bc.
[23] Xue, Pu, Si, Tong, Zhao, Huimin, Tawfik, DS. Optically guided mass spectrometry to screen microbial colonies for directed enzyme evolution. ENZYME ENGINEERING AND EVOLUTION: SPECIFIC ENZYME APPLICATIONSnull. 2020, 644: 255-273, https://www.webofscience.com/wos/woscc/full-record/WOS:000612553000012.
[24] 陈永灿, 张建志, 司同. 酿酒酵母中基于CRISPR/dCas9的基因转录调控工具的开发与应用. 生物技术通报[J]. 2020, 36(4): 1-12, http://lib.cqvip.com/Qikan/Article/Detail?id=7101582479.
[25] Si, Tong, Tian, Qiqi, Min, Yuhao, Zhang, Linzixuan, Sweedler, Jonathan, V, van der Donk, Wilfred A, Zhao, Huimin. Rapid Screening of Lanthipeptide Analogs via In-Colony Removal of Leader Peptides in Escherichia coli. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY[J]. 2018, 140(38): 11884-11888, https://www.webofscience.com/wos/woscc/full-record/WOS:000446142500002.
[26] Si, Tong, Li, Bin, Comi, Troy J, Wu, Yuwei, Hu, Pingfan, Wu, Yuying, Min, Yuhao, Mitchell, Douglas A, Zhao, Huimin, Sweedler, Jonathan V. Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY[J]. 2017, 139(36): 12466-12473, http://dx.doi.org/10.1021/jacs.7b04641.
[27] Tong Si, Ran Chao, Yuhao Min, Yuying Wu, Wen Ren, Huimin Zhao. Automated multiplex genome-scale engineering in yeast. NATURE COMMUNICATIONS[J]. 2017, 8(1): https://doaj.org/article/a7ce9e59cfef44bc9ab5ef2744240359.
[28] Chao, Ran, Mishra, Shekhar, Si, Tong, Zhao, Huimin. Engineering biological systems using automated biofoundries. METABOLIC ENGINEERINGnull. 2017, 42: 98-108, http://dx.doi.org/10.1016/j.ymben.2017.06.003.
[29] Chao, Ran, Liang, Jing, Tasan, Ipek, Si, Tong, Ju, Linyang, Zhao, Huimin. Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry. ACS SYNTHETIC BIOLOGY[J]. 2017, 6(4): 678-685, https://www.webofscience.com/wos/woscc/full-record/WOS:000400126500009.
[30] Si, Tong, Li, Bin, Zhang, Re, Xu, Yiran, Zhao, Huimin, Sweedler, Jonathan V. Characterization of Bacillus subtilis Colony Biofilms via Mass Spectrometry and Fluorescence Imaging. JOURNAL OF PROTEOME RESEARCH[J]. 2016, 15(6): 1955-1962, https://www.webofscience.com/wos/woscc/full-record/WOS:000377319200019.
[31] Li, Bin, Comi, Troy J, Si, Tong, Dunham, Sage J B, Sweedler, Jonathan V. A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms. JOURNAL OF MASS SPECTROMETRY[J]. 2016, 51(11): 1030-1035, https://www.webofscience.com/wos/woscc/full-record/WOS:000385865300006.
[32] Shi, Shuobo, Si, Tong, Liu, Zihe, Zhang, Hongfang, Ang, Ee Lui, Zhao, Huimin. Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae. SCIENTIFIC REPORTS[J]. 2016, 6: http://dx.doi.org/10.1038/srep25675.
[33] Si, Tong, Zhao, Huimin. A brief overview of synthetic biology research programs and roadmap studies in the United States. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY[J]. 2016, 1(4): 258-264, http://lib.cqvip.com/Qikan/Article/Detail?id=7103844686.
[34] Si, Tong, HamediRad, Mohammad, Zhao, Huimin. Regulatory RNA-assisted genome engineering in microorganisms. CURRENT OPINION IN BIOTECHNOLOGYnull. 2015, 36: 85-90, http://dx.doi.org/10.1016/j.copbio.2015.08.003.
[35] Li, Sijin, Si, Tong, Wang, Meng, Zhao, Huimin. Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening. ACS SYNTHETIC BIOLOGY[J]. 2015, 4(12): 1308-1315, https://www.webofscience.com/wos/woscc/full-record/WOS:000366884700006.
[36] Bao, Zehua, Xiao, Han, Lang, Jing, Zhang, Lu, Xiong, Xiong, Sun, Ning, Si, Tong, Zhao, Huimin. Homology-Integrated CRISPR-Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae. ACS SYNTHETIC BIOLOGY[J]. 2015, 4(5): 585-594, https://www.webofscience.com/wos/woscc/full-record/WOS:000354913000011.
[37] Si, Tong, Luo, Yunzi, Bao, Zehua, Zhao, Huimin. RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering. ACS SYNTHETIC BIOLOGY[J]. 2015, 4(3): 283-291, https://www.webofscience.com/wos/woscc/full-record/WOS:000351565600011.
[38] Si, Tong, Xiao, Han, Zhao, Huimin. Rapid prototyping of microbial cell factories via genome-scale engineering. BIOTECHNOLOGY ADVANCESnull. 2015, 33(7): 1420-1432, http://dx.doi.org/10.1016/j.biotechadv.2014.11.007.
[39] Si, Tong, Luo, Yunzi, Xiao, Han, Zhao, Huimin. Utilizing an endogenous pathway for 1-butanol production in Saccharomyces cerevisiae. METABOLIC ENGINEERING[J]. 2014, 22: 60-68, http://dx.doi.org/10.1016/j.ymben.2014.01.002.
[40] Liang, Youyun, Si, Tong, Ang, Ee Lui, Zhao, Huimin. Engineered Pentafunctional Minicellulosome for Simultaneous Saccharification and Ethanol Fermentation in Saccharomyces cerevisiae. APPLIED AND ENVIRONMENTAL MICROBIOLOGY[J]. 2014, 80(21): 6677-6684, https://www.webofscience.com/wos/woscc/full-record/WOS:000344160900012.
[41] Lian, Jiazhang, Si, Tong, Nair, Nikhil U, Zhao, Huimin. Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. METABOLIC ENGINEERING[J]. 2014, 24: 139-149, http://dx.doi.org/10.1016/j.ymben.2014.05.010.
[42] Du, Jing, Yuan, Yongbo, Si, Tong, Lian, Jiazhang, Zhao, Huimin. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. NUCLEIC ACIDS RESEARCH[J]. 2012, 40(18): e142-e142, [43] Sun, Jie, Wen, Fei, Si, Tong, Xu, JianHe, Zhao, Huimin. Direct Conversion of Xylan to Ethanol by Recombinant Saccharomyces cerevisiae Strains Displaying an Engineered Minihemicellulosome. APPLIED AND ENVIRONMENTAL MICROBIOLOGY[J]. 2012, 78(11): 3837-3845, https://www.webofscience.com/wos/woscc/full-record/WOS:000304185400007.
[44] Wang, Meng, Si, Tong, Zhao, Huimin. Biocatalyst development by directed evolution. BIORESOURCE TECHNOLOGY[J]. 2012, 115: 117-125, http://dx.doi.org/10.1016/j.biortech.2012.01.054.
[45] Jiang, Mo, Wong, Min Hao, Zhu, Zhilong, Zhang, Jieqian, Zhou, Lifang, Wang, Ke, Versypt, Ashlee N Ford, Si, Tong, Hasenberg, Lisa M, Li, YaoEn, Braatz, Richard D. Towards achieving a flattop crystal size distribution by continuous seeding and controlled growth. CHEMICAL ENGINEERING SCIENCE[J]. 2012, 77: 2-9, https://www.webofscience.com/wos/woscc/full-record/WOS:000305811500004.
[46] Cobb, Ryan E, Si, Tong, Zhao, Huimin. Directed evolution: an evolving and enabling synthetic biology tool. CURRENT OPINION IN CHEMICAL BIOLOGYnull. 2012, 16(3-4): 285-291, http://dx.doi.org/10.1016/j.cbpa.2012.05.186.

   

现指导学生

付立豪  博士研究生  071005-微生物学  

倪浩然  硕士研究生  086000-生物与医药