59. Critical Assessment of Protein Engineering (CAPE): A Student Challenge on the Cloud, Lihao Fu, Yuan Gao, Yongcan Chen, Yanjing Wang, Xiaoting Fang, Shujun Tian, Hao Dong, Yijian Zhang, Zichuan Chen, Zechen Wang, Shantong Hu, Xiao Yi*, Tong Si*, ACS Synthetic Biology, 2024, 13, 11, 3782–3787

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, Yongcan Chen,Erpeng Guo,Jianzhi Zhang, Tong Si*, Frontiers in Bioengineering and Biotechnology, 2020, 8:731

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