You are here:
Home
>>
PUBLICATIONS
- Papers
- Patents
Researcher Profile Link: ORCID, Google Scholar
# Co-First Authors ; * Corresponding Authors
- Under review, in revision, preprint
- At iSynbio, SIAT
58. Synthetic biology equipment: a tool to disrupt life technology, Tong Si, Xinhui Xing, Synth. Biol. J. 《合成生物学》, 2023, 4(5): 853-856 (in Chinese)
57. Applications of automated synthetic biotechnology in DNA assembly and microbial chassis manipulation, Yongcan Chen, Jianzhi Zhang*, Tong Si*, Synth. Biol. J. 《合成生物学》, 2023, 4(5): 857-876 (in Chinese)
56. RhlA exhibits dual thioesterase and acyltransferase activities during rhamnolipid biosynthesis, Ting Tang, Lihao Fu, Wenhao Xie, Yizhou Luo, Yating Zhang, Jianzhi Zhang*, Tong Si*, ACS Catalysis, 2023, 13: 5759–5766
55. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate, Songya Zhang, Lin Zhang, Anja Greule, Julien Tailhades, Edward Marschall, Panward Prasongpholchai, Daniel J. Leng, Jingfan Zhang, Jing Zhu, Joe A. Kaczmarski, Ralf B. Schittenhelm, Oliver Einsle, Colin J. Jackson, Fabrizio Alberti, Andreas Bechthold, Youming Zhang, Manuela Tosin*, Tong Si*, Max J. Cryle* Acta Pharmaceutica Sinica B，2023, 13(8), 3561-3574
54. Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects, Yongcan Chen, Ruyun Hu, Keyi Li, Yating Zhang, Lihao Fu, Jianzhi Zhang*, Tong Si*, ACS Synthetic Biology, 2023, 12, 5, 1461–1473
53. Biosynthesis of Hybrid Neutral Lipids with Archaeal and Eukaryotic Characteristics in Engineered Saccharomyces cerevisiae, Jianzhi Zhang, Tuo Li, Zhilai Hong, Chenfei Ma, Xiaoting Fang, Fengfeng Zheng, Wenkai Teng, Chuanlun Zhang, Tong Si*, Angewandte Chemie International Edition, 2023, 62(4), e202214344 (Selected as Hot Paper)
52. Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments, Ruyun Hu#*, Lihao Fu#, Yongcan Chen, Junyu Chen, Yu Qiao*, Tong Si*, Briefings in Bioinformatics, 2022, 24(1), bbac570
51. Robotic construction and screening of lanthipeptide variant libraries in Escherichia coli, Erpeng Guo, Lihao Fu, Xiaoting Fang, Wenhao Xie, Keyi Li, Zhiyu Zhang, Zhilai Hong*, Tong Si*, ACS Synthetic Biology, 2022, 11(12), 3900–3911
50. Enabling Technology and Core Theory of Synthetic Biology, Xian-En Zhang*, Chenli Liu*, Junbiao Dai*, Yingjin Yuan*, Caixia Gao*, Yan Feng*, Bian Wu*, Ping Wei*, Chun You*, Xiao-Wo Wang*, Tong Si*, SCIENCE CHINA Life Sciences, 2023, 66, https://doi.org/10.1007/s11427-022-2214-2
49. Enhanced rishirilide biosynthesis by a rare in-cluster phosphopantetheinyl transferase in Streptomyces xanthophaeus, Songya Zhang, Shuai Fan, Jing Zhu, Liying Zhou, Xiaohui Yan, Zhaoyong Yang, Tong Si*, and Tao Liu*, Microbiology Spectrum, 2022, 10(6), e0324722
48. Profiling of d-alanine production by the microbial isolates of rat gut microbiota, Cindy J. Lee#, Tian A. Qi#, Zhilai Hong#, Zhenkun Zhang, Yuhao Min, ,Linzixuan Zhang, Lei Dai, Huimin Zhao, Tong Si*, Jonathan V. Sweedler*, The FASEB Journal, 2022, 36(8), e22446
47. Directed evolution of a cyclodipeptide synthase with new activities via label-free mass spectrometric screening, Songya Zhang#, Jing Zhu#, Shuai Fan, Wenhao Xie, Zhaoyong Yang*, Tong Si*, Chemical Science, 2022, 13, 7581-7586
46. Towards one sample per second for mass spectrometric screening of engineered microbial strains, Lihao Fu#, Erpeng Guo#, Jianzhi Zhang, Keyi Li, Yongcan Chen*, Tong Si*, Current Opinion in Biotechnology, 2022, 76, 102725
45. Photobiocatalytic Solar Fuel and Solar Chemical Conversion: Sufficient Activity and Better Selectivity, Shulan Shi, Cuiping Zeng*, Tong Si*, Bo Wang, Po Keung Wong*, ACS ES&T Engineering, 2022, 2(6), 989–1000
44. Panoramic insights into semi-artificial photosynthesis: origin, development, and future perspective, Kemeng Xiao#, Jun Liang#, Xinyu Wang#, Tianfeng Hou, Xiaoning Ren, Panqing Yin, Zhiping Ma, Cuiping Zeng, Xiang Gao, Tao Yu, Tong Si, Bo Wang*, Chao Zhong*, Zhifeng Jiang*, Chun-Sing Lee, Jimmy Chai-mei Yu, Po Keung Wong, Energy & Environmental Science, 2022, 15, 529-549
43. Biosynthesis of Gut-Microbiota-Derived Lantibiotics Reveals a Subgroup of S8 Family Proteases for Class III Leader Removal, Yingying Zhang#, Zhilai Hong#, Liang Zhou#, Zhenkun Zhang, Ting Tang, Erpeng Guo, Jie Zheng, Ciji Wang, Lei Dai, Tong Si*, Huan Wang*, Angewandte Chemie International Edition, 2022, 61(6), e202114414
42. Prospective of synthetic biology database and intelligent data analysis, Ruyun Hu#, Yongcan Chen#, Jianzhi Zhang, Erpeng Guo, Lihao Fu, Yu Qiao*, Tong Si*, Chinese Bulletin of Life Sciences《生命科学》, 2021, 33(12), 1482-1492 (in Chinese)
41. High-Throughput Mass Spectrometry Complements Protein Engineering, Tong Si#,Pu Xue#, Kisurb Choe, Huimin Zhao*, Jonathan V. Sweedler*, In Protein Engineering: Tools and Applications, (H. Zhao, S.Y. Lee, J. Nielsen, G. Stephanopoulos Ed.) pp. 57-79, WILEY‐VCH GmbH, 2021
40. Genome-scale screening and combinatorial optimization of gene overexpression targets to improve cadmium tolerance in Saccharomyces cerevisiae, Yongcan Chen#, Jun Liang#, Zhicong Chen, Bo Wang* and Tong Si*, Frontiers in Microbiology, 2021, 12, 1922
39. Genomic and Metabolomic Investigation of a Rhizosphere Isolate Streptomyces netropsis WLXQSS-4 Associated with a Traditional Chinese Medicine, Songya Zhang, Lingxiao Zhang, Jing Zhu, Hong Chen, Zhicong Chen, Tong Si*, Tao Liu*, Molecules, 2021, 26(8), 2147
38. Accelerating strain engineering in biofuel research via build and test automation of synthetic biology, Jianzhi Zhang, Yongcan Chen, Lihao Fu, Erpeng Guo, Bo Wang, Lei Dai, Tong Si*, Current Opinion in Biotechnology, 2021, 67, 88-98
37. Insight into the tannic acid-based modular-assembly strategy based on inorganic–biological hybrid systems: a material suitability, loading effect, and biocompatibility study, Xiaoning Ren, Panqing Yin, Jun Liang, Xiangjian Liu, Wugen Zhan, Jiaojiao Niu, Tong Si, Tao Yu, Dan Wu, Bo Wang*, Materials Chemistry Frontiers, 2021, 5, 3867-3976
36. Recent Advances in the High-throughput Engineering of Lanthipeptides, Erpeng Guo, Jianzhi Zhang*, Tong Si*, China Biotechnology 《中国生物工程杂志》, 2021, 41(1), 30-41 (in Chinese)
35. Machine learning for synthetic biology: Methods and applications, Ruyun Hu#, Songya Zhang#, Hailin Meng, Han Yu, Jianzhi Zhang, Xiaozhou Luo, Tong Si*, Chenli Liu*, Yu Qiao*, Chinese Science Bulletin《科学通报》, 2020, 66(3), 284-299 (in Chinese)
34. Automation in synthetic biology using biological foundries, Ting Tang, Lihao Fu, Erpeng Guo, Zhenkun Zhang, Zining Wang, Chenfei Ma, Zhiyu Zhang, Jianzhi Zhang, Jiandong Huang*, Tong Si*, Chinese Science Bulletin 《科学通报》, 2020, 66(3), 300-309 (in Chinese)
33. Engineered Live Biotherapeutics: Progress and Challenges, Yang Tan, Juntao Shen, Tong Si, Chun Loong Ho, Yinqing Li, Lei Dai*, Biotechnol. J., 2020, 15(10), 2000155
32. Advances in RNAi-assisted strain engineering in Saccharomyces cerevisiae,
31. “Optically guided mass spectrometry to screen microbial colonies for directed enzyme evolution”, Pu Xue, Tong Si, Huimin Zhao*, in Methods Enzymol., 2020, 644, 255-273
30. Scalable enzyme mining via synthetic biology，Jianzhi Zhang, Lihao Fu, Ting Tang, Songya Zhang, Jing Zhu, Tuo Li, Zining Wang, Tong Si*, Synth. Biol. J. 《合成生物学》, 2020, 1-18 (in Chinese)
29. A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids. Pu Xue, Tong Si, Shekhar Mishra, Linzixuan Zhang, Kisurb Choe, Jonathan V Sweedler, Huimin Zhao*, Biotechnol. Bioeng .,2020, 117, 2131–2138
28. Development and applications of CRISPR/dCas9-based gene transcriptional regulation tool in Saccharomyces cerevisiae, Yongcan Chen, Jianzhi Zhang*, Tong Si*, Biotechnol. Bull.《生物技术通报》, 2020, 36(4), 1-12 (in Chinese)
27. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. Lihao Fu, Jianzhi Zhang*, Tong Si* BMC Energy, 2020, 2(1), 1-9
26. Whole‐Genome Regulation for Yeast Metabolic Engineering. Shuangying Jiang, Tong Si, Junbiao Dai* Small Methods, 2020, 4(2), 1900640
24. Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Tong Si#, Bin Li#, Troy J Comi#, Yuwei Wu, Pingfan Hu, Yuying Wu, Yuhao Min, Douglas A Mitchell, Huimin Zhao*, Jonathan V Sweedler*. J.
Am. Chem. Soc., 2017, 139(38), 12466-12473
23. Engineering biological systems using automated biofoundries. Ran Chao, Shekhar Mishra, Tong Si, Huimin Zhao*. Metab. Eng., 2017, 42, 92-108
22. Automated multiplex genome-scale engineering in yeast. Tong Si, Ran Chao, Yuhao Min, Yuying Wu, Wen Ren, Huimin Zhao*. Nat.
Commun., 2017, 8, 15187
21. Fully automated one-step synthesis of single-transcript TALEN pairs using a biological foundry. Ran Chao, Jing Liang, Ipek Tasan, Tong Si, Linyang Ju, Huimin Zhao*. ACS Synth. Biol., 2017, 6(4), 678-685
20. Strain Development by Whole-Cell Directed Evolution. Tong Si#, Jiazhang Lian#, Huimin Zhao*. In Directed Enzyme Evolution: Advances and Applications, (M. Alcalde Ed.) pp. 173-200, Springer International Publishing AG, 2017.
19. A brief overview of synthetic biology research programs and roadmap studies in the United States. Tong Si, Huimin Zhao*. Synth.
Sys. Biotechnol., 2016, 1(4), 258-264
18. A one‐step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms. Bin Li, Troy J Comi, Tong Si, Sage JB Dunham, Jonathan V Sweedler*. J. Mass Spectrum., 2016, 51(11), 1030-1035
17. Characterization of Bacillus subtilis Colony Biofilms via Mass Spectrometry and Fluorescence Imaging. Tong Si#, Bin Li#, Ke Zhang, Yiran Xu, Huimin Zhao*, Jonathan V Sweedler*. J.
Proteome Res.,2016, 15, 1955-1962
16. Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae. Shuobo Shi, Tong Si, Zihe Liu, Hongfang Zhang, Ee Lui Ang, Huimin Zhao*. Sci. Rep., 2016, 6, 25675
15. RNAi-Assisted Genome Evolution (RAGE) in Saccharomyces cerevisiae. Tong Si, Huimin Zhao*. In Methods in Molecular Biology, Volume 1470, pp. 183-198: High-Throughput RNAi Screening: Methods and Protocols, (D. Azorsa and S Arora, Eds.), Humana Press, 2016
14. Regulatory RNA-assisted genome engineering in microorganisms. Tong Si, Mohammad HamediRad, Huimin Zhao*. Curr. Opin. Chem. Biol., 2015, 36, 85-90
13. Rapid prototyping of microbial cell factories via genome-scale engineering. Tong Si#, Han Xiao#, Huimin Zhao*. Biotech. Adv., 2015, 33, 1420-1432
12. Development of a synthetic malonyl-CoA sensor in Saccharomyces cerevisiae for intracellular metabolite monitoring and genetic screening. Sijin Li, Tong Si, Meng Wang, Huimin Zhao*. ACS Synth. Biol., 2015, 4, 1308-1315
11. Homology-integrated CRISPR–Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. Zehua Bao, Han Xiao, Jing Liang, Lu Zhang, Xiong Xiong, Ning Sun, Tong Si, Huimin Zhao*. ACS Synth. Biol., 2015, 4, 585-594.
10. An engineered penta-functional minicellulosome for simultaneous saccharification and ethanol fermentation in Saccharomyces cerevisiae. Youyun Liang, Tong Si, Ee Lui Ang, Huimin Zhao*. Appl. Environ. Microbiol., 2014, 80, 6677-6684.
9. Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. Jiazhang Lian, Tong Si, Nikhil U Nair, Huimin Zhao*. Metab. Eng., 2014, 24, 139-149
8. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. Tong Si, Yunzi Luo, Zehua Bao, Huimin Zhao*. ACS
Synth. Biol., 2015, 4, 283-291
7. Utilizing an endogenous pathway for 1-butanol production in Saccharomyces cerevisiae. Tong Si, Yunzi Luo, Han Xiao, Huimin Zhao*. Metab.
Eng., 2014, 22, 60-68
6. Directed evolution: an evolving and enabling synthetic biology tool. Ryan E Cobb, Tong Si, Huimin Zhao*. Curr. Opin. Chem. Biol., 2012, 16, 285-91
5. Towards achieving a flattop crystal size distribution by continuous seeding and controlled growth. Mo Jiang, Min Hao Wong, Zhilong Zhu, Jieqian Zhang, Lifang Zhou, Ke Wang, Ashlee N Ford Versypt, Tong Si, Lisa M Hasenberg, Yao-En Li, Richard D Braatz*.Chem. Eng. Sci., 2012, 77, 2-9
4. Biocatalyst development by directed evolution. Meng Wang#, Tong Si#, Huimin Zhao*. Bioresour. Technol., 2012, 115, 117-25
3. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Jing Du#, Yongbo Yuan#, Tong Si, Jiazhang Lian, Huimin Zhao*. Nucleic Acid Res., 2012, 40, e142
2. Direct conversion of xylan to ethanol by recombinant Saccharomyces cerevisiae strains displaying an engineered mini-hemicellulosome. Jie Sun, Fei Wen, Tong Si, Huimin Zhao*. Appl. Environ. Microbiol., 2012, 78, 3837-45 (Highlighted in Nat. Chem. Bio., 2012, 8, 502)
1. O-GlcNAcylation modulates the self-aggregation ability of the fourth microtubule-binding repeat of tau. * Chun-Hui Yu, Tong Si, Wei-Hui Wu, Jia Hu, Jin-Tang Du, Yu-Fen Zhao, Yan-Mei Li*. Biochem.
Biophys. Res. Commun., 2009, 375, 20059-62
