李志远-生命科学联合中心

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中心PI

李志远

北京大学前沿交叉学院研究员/助理教授

生命科学联合中心PI

邮箱：zhiyuanli（AT）pku.edu.cn

实验室主页：http://cqb.pku.edu.cn/zyli/

研究领域：

本课题组致力用计算和理论方法解析复杂生物网络的自组织规律，特别关注微生物的铁相互作用网络,重点关注以下三大研究方向：

1. 从序列到分子的化学空间挖掘;

2. 微生态互作网络的重构与演化

3. 复杂生物系统的定量建模。

研究兴趣：以数理模型探索复杂生物网络的自组织规律

代表性研究成果：

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.