Selected Publications

17. Liu, R.^#, Pang, C ^#, Wu, G., He, B., Ren, H., Shen, Z., Liu, J., Song, ZM., Zhou, J.^* LI, Y.X.^* (2025). Harnessing P450 enzyme plasticity for generalizable peptide biaryl macrocyclization. bioRxiv, 2024-10.

16. Zhang, D., Shi, Y., Zhang, J., Liu, J., Wu, G., Zhang, J., Gao, Y., LI, Y.X.^* (2025). Systematically investigating and identifying unmodified bacteriocins in the human gut microbiome. Cell Genomics. In Revision

15. Chen, N.^#, Cai, P.^#,Lin, X.^#, Song, ZM, He, J., Li, Z, Zhang, D., . Li Z., Song, Y.^*. LI, Y.X.^* (2025). New Autoinducing Peptides Regulate Antibiotic Production for Sculpting Microbiome. Science Advances. 11,eadw5076

14. Song, ZM., Cai, C., Gao, Y., Lin, X., Wu, G., Zhuo, Q., Cai, P., Zhang, J.,, Liu, W., LI, Y.X.^* (2025). Decoding the Chemical Language of Ribosomally Synthesized and Post-Translationally Modified Peptides from the Untapped Archaea Domain. Angewandte Chemie International Edition. e202501074

13. Zhang, J.^#, Zhang, D.^#, Zhang, J., Gao, Y., Shi, Y., Cai, P., Zhong, Z., He, B., Li, X., Chen, M.^* and LI, Y.X.^* (2025). Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides. Nature Communications. 16, 3054

12. 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.

2024

11. 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 Nature Communications. 15，9371

10. 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

9. 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

8. 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.

2023

7. 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, 23, 15404–15416.

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

5. 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.(Editors' Highlights in Microbiology and infectious diseases)

4. 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.

3. 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.

2022

2. 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

1. 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  

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