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.

[2] 司同, 付立豪. 一种高通量制备用于质谱检测的微生物样品的取样装置. CN: CN218823255U, 2023-04-07.

[3] 胡如云, 乔宇, 司同. 一种机器学习引导的生物序列工程改造方法及装置. CN: CN115249514A, 2022-10-28.

   

[1] Songya Zhang, Lin Zhang, Anja Greule, Julien Tailhades, Edward Marschall, Panward Prasongpholchai, Daniel JLeng, Jingfan Zhang, Jing Zhu, Joe AKaczmarski, Ralf BSchittenhelm, Oliver Einsle, Colin JJackson, Fabrizio Alberti, Andreas Bechthold, Youming Zhang, Manuela Tosin, Tong Si, Max JCryle. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate. 药学学报:英文版. 2023, 第 18 作者13(8): 3561-3574, http://lib.cqvip.com/Qikan/Article/Detail?id=7110584173.
[2] 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[J]. 2023, 第 11 作者  通讯作者  66(8): 1742-1785, http://dx.doi.org/10.1007/s11427-022-2214-2.
[3] Chen, Yongcan, Hu, Ruyun, Li, Keyi, Zhang, Yating, Fu, Lihao, Zhang, Jianzhi, Si, Tong. Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects. ACS SYNTHETIC BIOLOGY[J]. 2023, 第 7 作者  通讯作者  12(5): 1461-1473, http://dx.doi.org/10.1021/acssynbio.2c00662.
[4] Tang, Ting, Fu, Lihao, Xie, Wenhao, Luo, Yizhou, Zhang, Yating, Zhang, Jianzhi, Si, Tong. RhlA Exhibits Dual Thioesterase and Acyltransferase Activities during Rhamnolipid Biosynthesis. ACS CATALYSIS[J]. 2023, 第 7 作者  通讯作者  13(8): 5759-5766, http://dx.doi.org/10.1021/acscatal.3c000465759.
[5] 陈永灿, 司同, 张建志. 自动化合成生物技术在DNA组装与微生物底盘操作中的应用. 合成生物学[J]. 2023, 第 2 作者4(5): 857-876, http://lib.cqvip.com/Qikan/Article/Detail?id=7110877240.
[6] 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, 第 6 作者  通讯作者  76: 
[7] 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, 第 6 作者  通讯作者  https://pubs.rsc.org/en/content/articlelanding/2022/SC/D2SC01637K.
[8] 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, 第 6 作者  通讯作者  http://dx.doi.org/10.1093/bib/bbac570.
[9] 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, 第 10 作者  通讯作者  61(6): http://dx.doi.org/10.1002/anie.202114414.
[10] 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, 第 9 作者  通讯作者  62(4): http://dx.doi.org/10.1002/anie.202214344.
[11] 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, 第 8 作者  通讯作者  11(12): 3900-3911, http://dx.doi.org/10.1021/acssynbio.2c00344.
[12] 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, 第 5 作者  通讯作者  12: http://dx.doi.org/10.3389/fmicb.2021.662512.
[13] 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, 第 10 作者  通讯作者  66(3): 300-309, http://lib.cqvip.com/Qikan/Article/Detail?id=7104239788.
[14] 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, 第 6 作者  通讯作者  26(8): http://dx.doi.org/10.3390/molecules26082147.
[15] 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, 第 3 作者  通讯作者  41(1): 30-41, http://lib.cqvip.com/Qikan/Article/Detail?id=7104036965.
[16] 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, 第 7 作者66(3): 284-299, https://www.sciengine.com/doi/10.1360/TB-2020-0456.
[17] 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, 第 10 作者  通讯作者  66(3): 300-309, 
[18] 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, 第 7 作者  通讯作者  66(3): 284-299, 
[19] 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, 第 7 作者5(10): 3867-3876, http://dx.doi.org/10.1039/d0qm00887g.
[20] 胡如云, 陈永灿, 张建志, 郭二鹏, 付立豪, 乔宇, 司同. 合成生物数据库与大数据智能分析展望. 生命科学[J]. 2021, 第 7 作者33(12): 1483-1492, http://lib.cqvip.com/Qikan/Article/Detail?id=7106780131.
[21] 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 BIOTECHNOLOGY. 2021, 第 7 作者  通讯作者  67: 88-98, http://dx.doi.org/10.1016/j.copbio.2021.01.010.
[22] 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, 第 2 作者117(7): 2131-2138, http://dx.doi.org/10.1002/bit.27343.
[23] Jiang, Shuangying, Si, Tong, Dai, Junbiao. Whole-Genome Regulation for Yeast Metabolic Engineering. SMALL METHODS. 2020, 第 2 作者4(2): https://www.webofscience.com/wos/woscc/full-record/WOS:000496824800001.
[24] 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, 第 8 作者1(3): 319-336, http://lib.cqvip.com/Qikan/Article/Detail?id=7102848985.
[25] Lihao Fu, Jianzhi Zhang, Tong Si. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. BMC ENERGY[J]. 2020, 第 3 作者2(1): 1-9, http://dx.doi.org/10.1186/s42500-020-0011-8.
[26] Tan, Yang, Shen, Juntao, Si, Tong, Ho, Chun Loong, Li, Yinqing, Dai, Lei. Engineered Live Biotherapeutics: Progress and Challenges. BIOTECHNOLOGY JOURNAL. 2020, 第 3 作者15(10): https://www.webofscience.com/wos/woscc/full-record/WOS:000568728800001.
[27] Chen, Yongcan, Guo, Erpeng, Zhang, Jianzhi, Si, Tong. Advances in RNAi-Assisted Strain Engineering inSaccharomyces cerevisiae. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY[J]. 2020, 第 4 作者  通讯作者  8: https://doaj.org/article/5ef85bc3bad145a49fcc0d1c1f9363bc.
[28] 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 APPLICATIONS. 2020, 第 2 作者644: 255-273, http://dx.doi.org/10.1016/bs.mie.2020.04.054.
[29] 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, 第 3 作者36(4): 1-12, http://lib.cqvip.com/Qikan/Article/Detail?id=7101582479.
[30] 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, 第 1 作者140(38): 11884-11888, https://www.webofscience.com/wos/woscc/full-record/WOS:000446142500002.
[31] 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, 第 1 作者139(36): 12466-12473, http://dx.doi.org/10.1021/jacs.7b04641.
[32] Tong Si, Ran Chao, Yuhao Min, Yuying Wu, Wen Ren, Huimin Zhao. Automated multiplex genome-scale engineering in yeast. NATURE COMMUNICATIONS[J]. 2017, 第 1 作者8(1): https://doaj.org/article/a7ce9e59cfef44bc9ab5ef2744240359.
[33] Chao, Ran, Mishra, Shekhar, Si, Tong, Zhao, Huimin. Engineering biological systems using automated biofoundries. METABOLIC ENGINEERING. 2017, 第 3 作者42: 98-108, http://dx.doi.org/10.1016/j.ymben.2017.06.003.
[34] 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, 第 4 作者6(4): 678-685, https://www.webofscience.com/wos/woscc/full-record/WOS:000400126500009.
[35] 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, 第 1 作者15(6): 1955-1962, https://www.webofscience.com/wos/woscc/full-record/WOS:000377319200019.
[36] 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, 第 3 作者51(11): 1030-1035, https://www.webofscience.com/wos/woscc/full-record/WOS:000385865300006.
[37] 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, 第 2 作者6: http://dx.doi.org/10.1038/srep25675.
[38] 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, 第 1 作者1(4): 258-264, http://lib.cqvip.com/Qikan/Article/Detail?id=7103844686.
[39] Si, Tong, HamediRad, Mohammad, Zhao, Huimin. Regulatory RNA-assisted genome engineering in microorganisms. CURRENT OPINION IN BIOTECHNOLOGY. 2015, 第 1 作者36: 85-90, http://dx.doi.org/10.1016/j.copbio.2015.08.003.
[40] 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, 第 2 作者4(12): 1308-1315, https://www.webofscience.com/wos/woscc/full-record/WOS:000366884700006.
[41] 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, 第 7 作者4(5): 585-594, https://www.webofscience.com/wos/woscc/full-record/WOS:000354913000011.
[42] Si, Tong, Luo, Yunzi, Bao, Zehua, Zhao, Huimin. RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering. ACS SYNTHETIC BIOLOGY[J]. 2015, 第 1 作者4(3): 283-291, https://www.webofscience.com/wos/woscc/full-record/WOS:000351565600011.
[43] Si, Tong, Xiao, Han, Zhao, Huimin. Rapid prototyping of microbial cell factories via genome-scale engineering. BIOTECHNOLOGY ADVANCES. 2015, 第 1 作者33(7): 1420-1432, http://dx.doi.org/10.1016/j.biotechadv.2014.11.007.
[44] Si, Tong, Luo, Yunzi, Xiao, Han, Zhao, Huimin. Utilizing an endogenous pathway for 1-butanol production in Saccharomyces cerevisiae. METABOLIC ENGINEERING[J]. 2014, 第 1 作者22: 60-68, http://dx.doi.org/10.1016/j.ymben.2014.01.002.
[45] 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, 第 2 作者80(21): 6677-6684, https://www.webofscience.com/wos/woscc/full-record/WOS:000344160900012.
[46] Lian, Jiazhang, Si, Tong, Nair, Nikhil U, Zhao, Huimin. Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. METABOLIC ENGINEERING[J]. 2014, 第 2 作者24: 139-149, http://dx.doi.org/10.1016/j.ymben.2014.05.010.
[47] Du, Jing, Yuan, Yongbo, Si, Tong, Lian, Jiazhang, Zhao, Huimin. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. NUCLEIC ACIDS RESEARCH[J]. 2012, 第 3 作者40(18): e142-e142, 
[48] Wang, Meng, Si, Tong, Zhao, Huimin. Biocatalyst development by directed evolution. BIORESOURCE TECHNOLOGY[J]. 2012, 第 2 作者115: 117-125, http://dx.doi.org/10.1016/j.biortech.2012.01.054.
[49] 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, 第 3 作者78(11): 3837-3845, https://www.webofscience.com/wos/woscc/full-record/WOS:000304185400007.
[50] 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, 第 8 作者77: 2-9, https://www.webofscience.com/wos/woscc/full-record/WOS:000305811500004.
[51] Cobb, Ryan E, Si, Tong, Zhao, Huimin. Directed evolution: an evolving and enabling synthetic biology tool. CURRENT OPINION IN CHEMICAL BIOLOGY. 2012, 第 2 作者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