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Teaching Staff

Professor LI, Philip Yong Xin

Professor LI, Philip Yong Xin

Associate Professor, Department of Chemistry, Faculty of Science, HKU

B.Sc. (Peking University); Ph.D. (HKUST)

  • 3910 2196
  • Room 305 Chong Yuet Ming Chemistry Building, University of Hong Kong, Pokfulam Road, Hong Kong

Research Interest

We are an enthusiastic team of chemical biology experts, dedicated to discovering innovative therapeutics by integrating cutting-edge deep learning techniques and synthetic biology. We are passionate about studying the chemical ecology of complex microbiota and the intricate "language" of host-microbe interactions. By gaining a deeper understanding of how microbes communicate and compete with microbe and host, we hope to unlock the cryptic chemistry of human microbiota for drug discovery, particularly focusing on ribosomal peptides.
Our mission is dual-pronged: we not only aim to intensify our understanding of chemical-mediated microbe-host interactions but also strive to harness the transformative power of artificial intelligence and synthetic biology. Our approach enables us to harness the immense potential of microbiota-derived peptides for drug discovery. Join us on this exciting mission to make a meaningful impact on the future of healthcare.
 

Research Topics

Natural Products, Chemical biology, Synthetic Biology, Deep Learning, Microbiota, Biosynthesis, Peptide drugs

 

Research Topics

Publications

  1. Zhang, D., Zou, Y., Shi, Y., Zhang, J., Liu, J., Wu, G., ... Chen, M* & Li, Y.X.* (2025). Systematically investigating and identifying bacteriocins in the human gut microbiome. Cell Genomics.100983
  2. Chen, N., Cai, P., Lin, X., Song, ZM, He, J., Li, Z, Zhang, D., . Li, Z., Song, Y.*. Li, Y.X.* (2025). Autoinducing Peptides Regulate Antibiotic Production to Potentially Shape Root Microbiome. Science Advance. 1(25), p.eadw5076.
  3. Song, Z.M., Cai, C., Gao, Y., Lin, X., Yang, Q., Zhang, D.,…,Jiang, H., Liu, W., and Li, Y.X.* (2025) Decoding the Chemical Language of Ribosomally Synthesized and Post-Translationally Modified Peptides from the Untapped Archaea Domain. Angew. Chem.-Int. Edit.e202501074
  4. Zhang, J. Zhang, D., Xu, Y., Zhang, J., Liu, R., Gao, Y., Shi, Y., Cai, P., Zhong, Z., He, B., Li, Y.X.,  Zhou, H., Chen M* and Li, Y.X.* (2025) Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides.Nat. Commun. 16, 3054.  
  5. Cheng Z., He B-B, Lei K, Gao Y, Shi Y, Zhong Z. Liu H, Liu. R, Zhang H, Wu S, Zhang W*, Tang X*. Li Y.X.* (2024). Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates. Nat. Commun.15, 4901. 
  6. Older, E. A.; Zhang, J.; Ferris, Z. E.; Xue, D.; Zhong, Z.; Mitchell, M. K.; Michael, M.; Wang, Y.; Chen, H.; Nagarkatti, P.; Nagarkatti, M.; Fan, D.; Ellermann, M.; Li, Y.X.* Li, J.* (2024). Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease. Nat. Commun. 15, 9371.
  7. He BB; Cheng, Z.; Zhong, Z.; Gao Y.; Liu, H.; Li, Y.X.* (2023). Bacterial Cytochrome P450 catalyzed Post-translational Macrocyclization. Angew. Chem. Int. Ed., e202311533. 
  8. Gao Y., Zhong Z., Zhang D., Zhang J., Li Y.X.*(2024). Ribosomal Peptides in Prokaryote-Phage Interactions through Deep Learning-Enabled Metagenome Mining. Microbiome. 12 (1), 94. 
  9. Zhang D, Zhang J, Kalimuthu S, Liu J, Song Z, He B, Cai P, Zhong Z, Feng C, Neelakantan P, Li YX* (2023). A systematic investigation of lactic acid bacteria-derived biosynthetic gene clusters reveals diverse antagonistic bacteriocins in the human microbiome. Microbiome. 11: 91.
  10. He BB, Cheng Z., Zhong Z., Gao Y., Liu H., and Li Y.X.*. (2022) "Expanded sequence space of radical S-adenosylmethionine-dependent enzyme involved in post-translational macrocyclization."  Angew. Chem. Int. Ed., 134(48), e202212447. 

 

Awards

  • 2024, Young Peptide Scientist Award (Chinese Peptide Society) 
  • 2024, Rising Star in Biological, Medicinal, and Pharmaceutical Chemistry (ACS Bio & Med Chem Au)
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