Research area:

Our laboratory is dedicated to decoding the complex interaction networks and self-organization of microbial communities across molecular, ecological, and evolutionary scales. Utilizing microbial secondary metabolism, specifically, the competition and cooperation for iron ("The Iron-Net"), as our quantitative anchor, we bridge data-driven computation, statistical physics, and experimental validation to explore:

1.Sequence-to-Molecule Mapping: Decoding the assembly logic of secondary metabolism (e.g., NRPS, PKS) to bridge the genotype-phenotype gap and discover chemical "dark matter" from genomic big data;

2.Microbial Ecology & Network Dynamics: Quantitatively uncover the physical and evolutionary laws governing competition, cooperation, and "cheating" in microbiomes;

Selected publications:

1. Linlong Yu, Guanyue Xiong, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. Systematic characterization of PBP2 as the primary siderophore recognizer in Actinomycetes and other Gram-positive bacteria. Microbial Genomics, 12(4):001671 (2026). doi: https://doi.org/10.1099/mgen.0.001671.

2. Shaohua Gu, Zhengying Shao, Zeyang Qu, Shenyue Zhu, Yuanzhe Shao, Di Zhang, Richard Allen, Ruolin He, Jiqi Shao, Guanyue Xiong, Alexandre Jousset, Ville-Petri Friman, Zhong Wei*, Rolf Kümmerli^*, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks. Science Advances, 11:eadq5038 (2025). doi: https://doi.org/10.1126/sciadv.adq5038.

3. Shaohua Gu, Jiqi Shao, Ruolin He, Guanyue Xiong, Zeyang Qu, Yuanzhe Shao, Linlong Yu, Di Zhang, Fanhao Wang, Ruichen Xu, Peng Guo, Ningbo Xi, Yinxiang Li, Yanzhao Wu, Zhong Wei, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. Forging the iron-net: Towards a quantitative understanding of microbial communities via siderophore-mediated interactions. Quantitative Biology, 13:2, e84. (2025). doi: https://doi.org/10.1002/qub2.84.

4. Shaohua Gu^#, Yuanzhe Shao^#, Karoline Rehm, Laurent Bigler, Di Zhang, Ruolin He, Ruichen Xu, Jiqi Shao, Alexandre Jousset, Ville-Petri Friman, Xiaoying Bian, Zhong Wei^*, Rolf Kümmerli^*, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways. eLife, 13:RP96719 (2024). doi: https://doi.org/10.7554/eLife.96719.3.

5. Ruolin He^#, Shaohua Gu^#, Jiazheng Xu, Xuejian Li, Haoran Chen, Zhengying Shao, Fanhao Wang, Jiqi Shao, Wen-Bing Yin, Long Qian^*, Zhong Wei^*, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. SIDERITE: Unveiling hidden siderophore diversity in the chemical space through digital exploration. iMeta (2024). doi: https://doi.org/10.1002/imt2.192.

6. Jiqi Shao, Nan Rong, Zhenchao Wu, Shaohua Gu, Beibei Liu, Ning Shen, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters. iScience, 26(9):107396 (2023). doi: https://doi.org/10.1016/j.isci.2023.107396.

7. Ruolin He, Jinyu Zhang, Yuanzhe Shao, Shaohua Gu, Chen Song, Long Qian, Wen-Bing Yin^*, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements. PLOS Computational Biology, 19(5):e1011100 (2023). doi: https://doi.org/10.1371/journal.pcbi.1011100.

8. Dan Shen^#, Jingyi Chu^#, Xiaolin Zhou^#, Zejun Lan, Rulan Zhang, Shuyu Wang, Haoxuan Tang, Yunrui Wang, Chenlei Hu, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*, Yan Song^*. Temporal neuronal differentiation programs safeguard neuronal diversity. Proceedings of the National Academy of Sciences, 123:e2527895123 (2026). doi: https://doi.org/10.1073/pnas.2527895123.

9. Xiaoyi Zhang, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*, Lei Zhang^*. Constructing a holistic map of cell fate decision by hyper solution landscape. Cell Systems, 17(4):101562 (2026). doi: https://doi.org/10.1016/j.cels.2026.101562 .

10. Gang Xue, Xiaoyi Zhang, Wanqi Li, Lu Zhang, Zongxu Zhang, Xiaolin Zhou, Di Zhang, Lei Zhang^*, 𝐙𝐡𝐢𝐲𝐮𝐚𝐧 𝐋𝐢^*. A logic-incorporated gene regulatory network deciphers principles in cell fate decisions. eLife, 12:RP88742 (2024). doi: https://doi.org/10.7554/eLife.88742.3.