Author

Ruichen Xu

Peking University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Genomics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 3 Research Focus:benchmarking· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Research Focus:database / resource· 1 Assay:DNA methylation· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Ruolin HeiD· 3 shared Zhiyuan LiiD· 3 shared Guanyue XiongiD· 2 shared Jiqi ShaoiD· 2 shared Shaohua GuiD· 2 shared Shizheng Tian· 2 shared Xiaoying BianiD· 2 shared Yuanzhe ShaoiD· 2 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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3 shared papersSystems Biology

Ruolin HeORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Coevolution-driven reconstruction of multi-taxa siderophore interaction networks reveals topological diversity of microbial exploitation

Guanyue Xiong, Ruichen Xu, Yukun Zheng, Linlong Yu, Yufei Qiao, Shizheng Tian, Binglei Wang, Ruolin He, Zihao Yang, Xiaoying Bian, Yang Bai, Huimin Yu, Zhiyuan Li

The paper introduces CIM, a method to predict CFM-Rec interactions from genomic data, revealing topological patterns in microbial communities.

bioRxiv · Jul 29, 2026 · PreprintSystems Biology

Functional-space alignment resolves the eco-evolutionary landscape of siderophore biosynthesis across bacteria

Jiqi Shao, Yanzhao Wu, Shizheng Tian, Ruichen Xu, Haohua Luo, Yuanzhe Shao, Shaohua Gu, Ruolin He, Guanyue Xiong, Peng Guo, Nan Rong, Zhong Wei, Zhiyuan Li

The paper develops a functional-space framework to analyze siderophore biosynthesis across bacteria, revealing ecological drivers over phylogenetic constraints.

bioRxiv · Mar 9, 2025 · PreprintBioinformatics

From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

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

The paper develops a bioinformatic pipeline to predict bacterial siderophore structures and receptors from genome sequences, revealing significant diversity in pyoverdines and their receptors.

eLife · Oct 1, 2024Peer-reviewedGenomics