YONG-XIN LI'S LAB
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Harnessing AI for Genome Mining
Peptide Biosynthesis and bioengineering
Deciphering the Chemistry of Microbiota
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Dr. Yong-Xin Li
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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
Full list of publications
Home
Research
Harnessing AI for Genome Mining
Peptide Biosynthesis and bioengineering
Deciphering the Chemistry of Microbiota
People
Dr. Yong-Xin Li
Lab Members
Alumni
Gallery
Publications
Join us