All Publications

51. Song, ZM., Cai, C., Gao, Y., Lin, X., Wu, G., Zhuo, Q., Cai, P., Zhang, J.,, Liu, W., LI, Y.X.^* (2024). Deciphering the chemical landscape and potential ecological function of RiPPs from the untapped Archaea domain. bioRxiv, 2024-10.

50. Liu, R.^#, Ren, H.^#, Wu, G., He, B., Pang, C., Shen, Z., Liu, J., Song, ZM., Zhou, J.^* LI, Y.X.^* (2024). P450-Catalyzed Biaryl Macrocyclization of Leaderless Ribosomal Peptides. bioRxiv, 2024-10.

49. Zhang, D., Shi, Y., Zhang, J., Liu, J., Wu, G., Zhang, J., Gao, Y., LI, Y.X.^* (2024). Systematically investigating and identifying unmodified bacteriocins in the human gut microbiome. bioRxiv, 2024-07.

48. Zhang, J.^#, Zhang, D.^#, Zhang, J., Gao, Y., Shi, Y., Cai, P., Zhong, Z., He, B., Li, X. and LI, Y.X.^* (2024). Elucidating the Diversity and Potential Function of Ribosomally Synthesized and Post-translationally Modified Peptides in the Human Microbiome. bioRxiv, 2024-07.

47. Ma, X.^# Zhang, J.^# Jiang, Q. and LI, Y.X.^*, Yang, G.^* (2025). Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry. eBioMedicine, 111.

46. Zdouc, Mitja M., Kai Blin, Nico LL Louwen, Jorge Navarro, Catarina Loureiro, Chantal D. Bader, Constance B. Bailey et al. (2024) "MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration." Nucleic Acids Research, gkae1115

45. Liu, J., Liu, R., He, B. B., Lin, X., Guo, L., Wu, G，LI, Y.X.^* (2024). Bacterial Cytochrome P450 Catalyzed Macrocyclization of Ribosomal Peptides. ACS Bio & Med Chem Au. Invited review

44. 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 negatively associates TLR4-antagonizing sulfonolipids with inflammatory bowel disease Nature Communications. 15，9371

43. Chen, N.; Cai, P.;Zhang, D.; Zhang, J.; Zhong, Z.; LI, Y.X.^* (2024). Metabolic Engineering of “Last-line Antibiotic” Colistin in Paenibacillus polymyxa. Metabolic Engineering. 85, 35-45

42. Gao, Y.^#; Zhong, Z.^#;Zhang, D.; Zhang, J.;Li, Y.X.^*(2024).Exploring the Roles of Ribosomal Peptides in Prokaryote-Phage Interactions through Deep Learning-Enabled Metagenome Mining. Microbiome, 12, 94.

41. Cheng, Z; He, BB.; Lei, K.Gao, Y.; Shi, YQ.; Zhong, Z.;Liu, HY.; Liu, RZ.;Zhang, H; Wu, S., Zhang, W.^* Tang, XY.^*;Li, Y.X.^*(2024).Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates. Nature Communications. 15, 4901

40. Cai, PY; He, JZ.; Song, ZM.; Tian, YQ.; Zhong, Z.;Zhang, DW.; Shi, YQ.;Tang, XY.;LI, Y.X.^* (2023). Uncovering Untapped Carboxylic Acid Reductases (CARs) for One-Step Biosynthesis and Diversification of Bioactive Nitrogen-containing Heterocycles. ACS Catalysis. 13, XXX, 15404–15416.

39. He BB^#;Liu J^#; Cheng, Z.;Liu, R.; Zhong, Z.; Gao Y.; Liu, H.;Song,Z.M.; LI, Y.X.^* (2023). Bacterial Cytochrome P450 Catalyzed Post-translational Macrocyclization of Ribosomal Peptides Angewandte Chemie International Edition. e202311533. Hot Paper!

38. Li, Y.^#, Zhang, D.^#, Wang, M., Jiang, H.^*, Feng, C.^* LI, Y.^* (2023). Intratumoral microbiota is associated with prognosis in patients with adrenocortical carcinoma. iMeta , e102.

37. Ding, W., Wang, S., Qin, P., Fan, S., Su, X., Cai, P.,... LI, Y.X.^* Zhang, W.^* (2023). Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms. Nature Communications , 14(1), 2033.

36. Dengwei Zhang, Jian Zhang, Shanthini Kalimuthu, Jing Liu, Zhiman Song, Beibei He, Peiyan Cai, Zheng Zhong, Chenchen Feng, Prasanna Neelakantan, Yong-Xin Li^* (2023). A systematic investigation of lactic acid bacteria-derived biosynthetic gene clusters reveals diverse antagonistic bacteriocins in the human microbiome. Microbiome, 11: 91.

35. Haoyu Liang^#, Zhiman Song^#, Zheng Zhong, Dengwei Zhang, Wei Yang, Le Zhou, Ethan Older, Jie Li, Huan Wang, Zhirui Zeng^*, Yong-Xin Li^*, (2023). Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea. Microbiome, 11: 74.

34. Dan Xue, Zhuo Shang, Ethan A. Older, Zheng Zhong, Conor Pulliam, Kyle Peter, Mitzi Nagarkatti, Prakash Nagarkatti, Yong-Xin Li, Jie Li (2023). Refactoring and Heterologous Expression of Class III Lanthipeptide Biosynthetic Gene Clusters Lead to the Discovery of N,N-Dimethylated Lantibiotics from Firmicutes. ACS Chemical Biology. 18, 3, 508–517

33. Barbara R. Terlouw, Kai Blin, ..., Yong-Xin Li, ..., Zheng Zhong, ..., Tilmann Weber, Marnix H. Medema. (2023). MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Research, 51(D1), D603-D610.

32. Bei-bei He, Zhuo Cheng, Zheng Zhong, Ying Gao, Hongyan Liu, Yong-Xin Li (2022). Expanded Sequence Space of Radical S-Adenosylmethionine-Dependent Enzymes Involved in Post-translational Macrocyclization. Angewandte Chemie International Edition, e202212447

31. Dan Xue^#, Ethan A. Older^#, Zheng Zhong^#, Zhuo Shang, Nanzhu Chen, Nolan Dittenhauser, Lukuan Hou, Peiyan Cai, Michael D. Walla, Shi-Hui Dong, Xiaoyu Tang, Prakash Nagarkatti, Mitzi Nagarkatti, Yong-Xin Li^*, Jie Li^* (2022). Correlational networking guides the discovery of unclustered lanthipeptide protease-encoding genes. Nature communications, 13, 1647  

30. Karol Al Ayed, Ross D. Ballantine, Michael Hoekstra, Samantha J. Bann, Charlotte M. J. Wesseling, Alexander T. Bakker, Zheng Zhong, Yong-Xin Li, Nora C. Brüchle, Mario van der Stelt, Stephen A. Cochrane, Nathaniel I. Martin (2022). Synthetic studies with the brevicidine and laterocidine lipopeptide antibiotics including analogues with enhanced properties and in vivo efficacy. Chemical Science, 13, 3563-3570.

29. Fan, S., Wang, M., Ding, W., Li, Y. X., Zhang, Y. Z., & Zhang, W. (2021). Scientific and technological progress in the microbial exploration of the hadal zone. Marine Life Science & Technology, 1-11.

28. Long, L., Wang, R., Chiang, H. Y., Ding, W., Li, Y. X.^*, Chen, F.^*, & Qian, P. Y.^* (2021). Discovery of Antibiofilm Activity of Elasnin against Marine Biofilms and Its Application in the Marine Antifouling Coatings. Marine drugs, 19(1), 19.

27. Li, C. ,Li, Y.X., Qin, G., Chen, Z., Qu, M., Zhang, B., Han, X., Wang, X., Qian, P.Y. and Lin, Q. (2020). The regulatory role of retinoic acid in male pregnancy of the seahorse. The Innovation, 100052.

26. Zhong, Z.^#, He, B.^#, Li, J., & Li, Y. X. (2020). Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs). Synthetic and Systems Biotechnology, 5(3), 155-172. (invited review)

25. Bann, S. J., Ballantine, R. D., McCallion, C. E., Qian, P. Y., Li, Y., & Cochrane, S. A. (2019). A Chemical-Intervention Strategy to Circumvent Peptide Hydrolysis by D-Stereoselective Peptidases. Journal of medicinal chemistry, 62(22), 10466-10472.

Publications before joining HKU:

24. ​Zhang, W., Watanabe, H. K., Ding, W., Lan, Y., Tian, R. M., Sun, J., Chen, C. Li, Y.X., ... & Toyofuku, T. Gut microbial divergence between two populations of the hadal amphipod Hirondellea gigas. Appl. Environ. Microbiol., 2019, 85(1), e02032-18.

23. ​Zhang, W., Ding, W., ​Li, Y. X., Tam, C., Bougouffa, S., Wang, R., ... & Sun, J. Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nature communications, 2019, 10(1), 517.

22. Li YX^#, Zhong Z^#, Zhang W, Qian PY. Discovery of cationic nonribosomal peptides as Gram-negative antibiotics through global genome mining. Nature Communications, 2018,9(1): 3273.  (Editor’s Highlights paper in Therapeutics， Recommended by F1000 Prime as ‘the first discovery of an antibiotic from a genomics approach that shows efficacy in treating a systemic infection’).

21. ​Ballantine, R.D., ​Li, Y.X., Qian, P.Y. and Cochrane, S.A. Rational design of new cyclic analogues of the antimicrobial lipopeptide tridecaptin A 1. Chemical Communications, 2018, 54(75), pp.10634-10637.

20. ​Li YX, Zhong Z, Hou P, Zhang W, Qian PY. Resistance to nonribosomal peptide antibiotics mediated by D-stereospecific peptidases. Nature Chemical Biology, 2018, 14(4), 381-385. (Highlighted by: F1000 Prime, Xinhua News, TVB News, BTV News, AsiaScientist, Science Daily, Science Newsline, EurekAlert, and more than ten local Newspapers of Hong Kong).

19. ​Zhang W, Tian RM, Sun J, Bougouffa S, Ding W, Cai L, Lan Y. Tong H, Li YX, Jamieson AJ and Bajic VB, Drazen JC, Bartlett D, Qian PY . Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point. MSystems, 2018 3: e00009-18.

18. ​Li Z, Li J, Gu JP, Lai JYH, Duggan BM, Zhang WP, Li ZL, LiYX, RB Tong, Moore B, & Qian PY, Discovery of precolibactin-886, the missing aminomalonate-containing member of the genotoxin colibactin family. Nature Chemical Biology, 2016 12(10): 773–775.

17. ​Li ZR, Li YX, Lai JYH, Tang J, Wang B, Lu L, Zhu G, Wu X, Xu Y, Qian PY. Critical Intermediates Reveal New Biosynthetic Events in the Enigmatic Colibactin Pathway. ChemBioChem, 2015, 16(12), 1715-1719.

16. ​Li YX, Li Z, Yamanaka K, Xu Y, Zhang W, Vlamakis H, Kolter R, Moore BS, Qian PY. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. Scientific reports, 2015, 5:9383.

15. ​Qian PY, Li Z, Xu Y, Li YX, Fusetani N. Mini-review: Marine natural products and their synthetic analogs as antifouling compounds: 2009–2014. Biofouling, 2015, 31(1), 101-122.

14. ​Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li YX, Cai L, Wong YH, ... & Qian PY. Synchronized dynamics of bacterial niche‐specific functions during biofilm development in a cold seep brine pool. Environmental microbiology, 2015, 17, 4089–4104.

13. ​Wang KL, Xu Y, Lu L, Li YX, Han Z, Zhang J, ... & Qian PY. Low-Toxicity Diindol-3-ylmethanes as Potent Antifouling Compounds. Marine Biotechnology, 2015, 17(5), 624-632.

12. ​Lu L, Wang J, Xu Y, Wang K, HuY., Tian R, Li YX, ... & PY., Qian. A High-Resolution LC-MS-Based Secondary Metabolite Fingerprint Database of Marine Bacteria. Scientific reports, 2014, 4, 6537.

11. ​Zhang W, Wang Y, Lee OO, Tian R, Cao H, Gao Z, Li YX, L Yu, Y Xu, Pei-Yuan QianAdaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses, Scientific reports, 2013, 3, 3180.

10. ​Liu LL, He LS, Xu Y, Han Z, Li YX, Zhong JL, Guo XR, Zhang XX, Ko KM, Qian PY.  Caspase-3-Dependent Apoptosis of Citreamicin ε-Induced HeLa Cells Is Associated with Reactive Oxygen Species Generation, Chem. Res. Toxicol., 2013, 26(7), 1055–1063.

9. ​Li YX#, Wu HX#, Xu Y, Shao CL, Wang CY, Qian PY. Antifouling activity of secondary metabolites isolated from Chinese marine organisms. Marine Biotechnology, 2013, 15(5):552-558. 

8. ​Li YX, Xu Y, Liu L, Han Z, Lai PY, Guo X, Zhang X, Lin W, Qian PY. Five new amicoumacins isolated from a marine-derived bacterium Bacillus subtilis. Marine drugs, 2012, 10(2):319-28.7.

7. ​Li YX, Zhang F, Xu Y, Matsumura K, Han Z, Liu L, Lin W, Jia Y, Qian PY. Structural optimization and evaluation of butenolides as potent antifouling agents: modification of the side chain affects the biological activities of compounds. Biofouling, 2012, 28(8):857-64. 

6. ​Li YX, Yu S, Liu D, Proksch P, Lin W. Inhibitory effects of polyphenols toward HCV from the mangrove plant Excoecaria agallocha L. Bioorganic & medicinal chemistry letters, 2012, 22(2):1099-102.

5. ​Han Z, Xu Y, McConnell O, Liu LL, Li YX, Qian PY. Two antimycin A analogues from marine-derived Actinomycete Streptomyces lusitanus, Marine drugs, 2012, 10, 668-676.

4. ​Liu LL, Xu Y, Han Z, Li YX, Lu L, Lai PY, Zhong JL, Guo XR, Zhang XX, Qian PY. Four New Antibacterial Xanthones from the Marine-Derived Actinomycetes Streptomyces caelestis. Marine Drugs, 2012, 10, 2571-2583.

3. ​Lai DW, Li YX, Xu Mj, Deng ZW, Ofwegen LV, Qian PY, WH Lin. Sinulariols A–S, 19-oxygenated cembranoids from the Chinese soft coral Sinularia rigida, Tetrahedron, 2011, 67, 6018-6029.

2. ​Li YX, Liu J, Yu S, Proksch P, Gu J, Lin W. TNF-α inhibitory diterpenoids from the Chinese mangrove plant Excoecaria agallocha L. Phytochemistry, 2010, 71:2124-31.

1. ​LI YX, Yu X, Yu SJ, Lin WH. Phenolic glucopyranosides from the Chinese mangrove plant Excoecaria agallocha, J. Chin. Pharm. Sci., 2010, 19, 256-259.