Yaojun Tong

  • Tel: +86-21-34204266
  • Email: yaojun.tong@sjtu.edu.cn
  • Address: Room 3-409, Biopharmacy Building, Dongchuan Road 800, Minhang District, Shanghai 200240, China
  • Prof. Tong is interested in microbial synthetic biology. He has published 49 papers with near 4000 citations and an H-index of 28. He serves as Associate Editor of Synthetic and Systems Biotechnology, a committee member of IMES ECC, Chair of the Metabolic Engineering and Biomanufacturing Committee of CSM, and a Reviewer for NOW and CZI.

Education and Research Experience

  • 2020.12-present, School of Life Sciences and Technology, Shanghai Jiao Tong University, Tenure-track Associate Professor.
  • 2016.02-2020.12, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark. Researcher (Assistant Professor)
  • 2013.09-2016.02, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark. Postdoc, working with Prof. Sang Yup Lee, and Prof. Tilmann Weber.
  • 2008.09-2013.09, Institute of Microbiology, Chinese Academy of Sciences, PhD.
  • 2004.09-2008.06, University of Science and Technology, Beijing, BSc.

Research Interests

1. Advanced synthetic biology tools development for microbes.

CRISPR-based genome editing toolkit, tuneable regulation platform of transcription and translation, etc.

2. Intelligent microbial cell factory design and construction.

Design and construct microbial chassis strains for bio-production, bio-remediation, and bio-therapy.

3. Sociomicrobiology study to enable next generation biotechnology.

Study the individual behavior of microbes within a colonized society, investigating possibilities of developing new biotechnology.

Selected Publications

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    Luo, J., Chia, N., Qin, Y., Tan, P., Zhang, L., Yang, S., Yuan, Z., Hong, L., Lee, S. L.*, Tong, Y.* STAGE: A compact and versatile TnpB-based genome editing toolkit for Streptomyces, Proc. Natl. Acad. Sci. U.S.A. 122 (35) e2509146122. (2025).

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    Tan, W., Tong, S., Gao, Y., Wang, J., Zhang, J., Xie, Z., Dai, H., Liang, Y., Tan, G.-Y., Zhang, L.*, Tong, Y.*, Rational spatial rewiring of key enzymes enhances α-santalene production in Saccharomyces cerevisiae. Bioresour. Technol. 436,133027. (2025).

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    Liang, Y., Tong, S., Zhang, J., Tan, G.-Y., Zhang, L., Lee, S. Y.*, Tong, Y.* Expanding horizons of CRISPR applications beyond genome editing. Trends Genet. 41, 10, 934-953. (2025).

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    Luo, J., Li, N., Wang, W., Gao, Y., Tang, H.*, Bai, L.*, Lee, S. Y.*, Tong, Y.*, Halogenases and dehalogenases: mechanisms, engineering, and applications. Nat. Prod. Rep. doi: 10.1039/D5NP00055F. (2025).

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    Yang, S., Cai, Z., Chia, N., Luo, L., Weber, T.*, Blin, K.*, Tong, T.*, CRISPy-web 3.0: a unified platform for multi-modal guide RNA design for CRISPR and TnpB genome editing applications. Synth. Syst. Biotechnol. 11, 317-322. (2025).

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    Tong, Y.*, Jørgensen, T.S., Whitford, C.M., Weber, T.*, Lee, S.Y.* A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing. Nature Communications. 12, 5206 (2021).

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    Tong, Y.*, #, Zhang, J.#, Sun, N. #, Wang, X. #, Wei, Q., Zhang, Y., Huang, R., Pu, Y., Dai, H., Ren, B., Pei, G., Song, F., Zhu, G., Wang, X., Xia, X., Chen, X., Jiang, L., Zhang, J., Ouyang, L., Zhang, B., Jiang, Y., Liu, X., Calderone, R., Bai, F.*, Zhang, L.*, Alterovitz, G. Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p. Science Bulletin. 66, 1895-1905. (2021).

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    Tong, Y., Whitford, C. M., Blin, K., Jørgensen, T. S., Weber, T.*, Lee, S. Y.* CRISPR-Cas9-based, CRISPRi, and CRISPR-BEST-mediated genetic manipulation in streptomycetes. Nature Protocols. 15, 2470-2502. (2020).

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    Tong, Y., Whitford, C. M., Robertsen, H. L., Blin, K., Jørgensen, T. S., Klitgaard, A. K., Weber, T.*, Lee, S. Y.* Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST. Proc. Natl. Acad. Sci. U.S.A., 116, 20366-20375 (2019).

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    Tong, Y., Charusanti, P., Zhang, L., Weber, T.*, Lee, S. Y.* CRISPR-Cas9 Based Engineering of Actinomycetal Genomes. ACS Synth. Biol. 4, 1020-1029 (2015). Journal cover paper. ESI highly cited paper.

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Students