Ruichen Xu

HP-JEPA: Hierarchical Partitioning for Multi-Resolution Graph Joint-Embedding Predictive Learning

Ruichen Xu, Jingxiang Qu, Wenhan Gao, Jiaxing Zhang et autres

Graph self-supervised learning aims to learn transferable representations from large-scale unlabeled graph data. Joint-embedding predictive architectures (JEPAs) avoid explicit negative-pair construction and raw-input reconstruction by predicting masked targets directly in latent space. However, existing graph JEPAs typically rely on a single predefined …

HP-JEPA: Hierarchical Partitioning for Multi-Resolution Graph Joint-Embedding Predictive Learning

Ruichen Xu, Jingxiang Qu, Wenhan Gao, Jiaxing Zhang et autres

Graph self-supervised learning aims to learn transferable representations from large-scale unlabeled graph data. Joint-embedding predictive architectures (JEPAs) avoid explicit negative-pair construction and raw-input reconstruction by predicting masked targets directly in latent space. However, existing graph JEPAs typically rely on a single predefined …

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

Guanyue Xiong, Ruichen Xu, Yukun Zheng, Linlong Yu et autres

Abstract Microbial communities are shaped by secreted metabolites that mediate ecological interactions, yet predicting these interactions from genomic sequences remains difficult, because the specific recognition between co-functional metabolites (CFMs), such as siderophores, and their receptor proteins (Rec) cannot be inferred from gene …

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First-Principles Study on Structural, Magnetic, Dynamical, and Mechanical Properties of the All-d Transition Metal Fe2ZrPt Full-Heusler Alloys

Ruichen Xu, Guoliang Yu, Xi Zhang, 成泰民

Heusler alloys are pivotal for functional materials, yet the all-d transition metal Fe2ZrPt full-Heusler alloy remains rarely studied. Herein, first-principles calculations are employed to systematically explore the structural, thermodynamic, lattice dynamical, mechanical, magnetic, and electronic properties of Fe2ZrPt alloy with Fm $$\bar …

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Structural prediction and physical properties of ferromagnetic Fe3Ni2 alloys

Guoliang Yu, Ruichen Xu, Xinxin Zhang, Taimin Cheng

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Accessing Underexplored Biosynthetic Potential by Initiation Unit Engineering of Nonribosomal Peptide Synthetases in Proteobacteria

Xianping Bai, Lin Zhong, Ying Liu, Hanna Chen et autres

Nonribosomal peptide synthetases (NRPSs) represent a valuable yet underexplored resource for producing bioactive natural products. However, most NRPSs remain silenced potentially due to factors such as dysfunction of the initiation unit. The starter condensation (Cs) domain of the initiation unit catalyzes the …

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

Jiqi Shao, Yanzhao Wu, Ruichen Xu, Shaohua Gu et autres

Abstract Siderophores are central mediators of microbial iron acquisition, competition, and ecological adaptation, yet their biosynthetic diversity remains difficult to resolve across species because existing sequence-based BGC comparison is strongly constrained by phylogenetic background. Here we combine large-language-model-assisted literature mining, functional-space comparison, …

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Forging the iron‐net: Towards a quantitative understanding of microbial communities via siderophore‐mediated interactions

Shaohua Gu, Jiqi Shao, Ruolin He, Guanyue Xiong et autres

Abstract Iron is a critical yet limited nutrient for microbial growth. To scavenge iron, most microbes produce siderophores—diverse small molecules with high iron affinities. Different siderophores are specifically recognized and uptaken by corresponding recognizers, enabling targeted interventions and intriguing cheater‐producer dynamics. We …

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Author response: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Shaohua Gu, Yuanzhe Shao, Karoline Rehm, Laurent Bigler et autres

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Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Shaohua Gu, Yuanzhe Shao, Karoline Rehm, Laurent Bigler et autres

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be …

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The physical properties of crystalline iron-rich silicides

Y. D. Wang, Ruichen Xu, Xiaofei An, Yubo Zang et autres

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Author response: 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 et autres

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be …

fi, ch, cn (code pays fourni par la source)