Author

Xinyu Wang

University of Amsterdam

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

Same name, identified by ORCID

Biology Disciplines

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Microbiology· 3 Bioinformatics· 2 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 5 Approach:deep learning· 3 Approach:experimental assay· 3 Organism:human· 3 Assay:whole-genome sequencing· 3 Organism:bacteria (other)· 2 Research Focus:software / tool· 2 Approach:statistical model· 2

Frequent Co-Authors

Benno H. ter KuileiD· 3 shared Martijs J. JonkeriD· 3 shared Wim C. de LeeuwiD· 3 shared Luyuan Nong· 2 shared Alphonse de Koster· 1 shared Belinda B. Koenders· 1 shared Bo Dong· 1 shared Bo ZhangiD· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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3 shared papersMicrobiology

Benno H. ter KuileORCID

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

AI-driven discovery and engineering of human endogenous nanocage proteins for mRNA delivery

Dongmin Xun, Lanqing Li, Jie Zou, Yi Liu, Ziyue Yang, Qianyi Liang, Ke Li, Zhu Zhu, Jicong Zhang, Lijun Lang, Kun Liu, Xinyu Wang, Meilin Tian, Guangyong Chen, Bolin An, , Chao Zhong

The paper develops DeepDelivery, an AI platform that identifies human proteins for mRNA delivery, validating 80% of top candidates for efficient, non-inflammatory delivery.

Nature Communications · Oct 31, 2026Peer-reviewedSynthetic Biology

Unbalanced Perturbation Dynamics For Cell Fate Design

Qiangwei Peng, Yuchuan Wang, Jianzhe Li, Xinyu Wang, Yao Xiao, Peijie Zhou

This paper introduces U-Pert, a framework for modeling unbalanced perturbation dynamics in single-cell data, enabling forward prediction and inverse design of cellular interventions.

bioRxiv · Jul 4, 2026 · PreprintBioinformatics

Modulation of rob expression accelerates development of antibiotic resistance in Yersinia enterocolitica

Xinyu Wang, Taichi Chen, Martijs J. Jonker, Alphonse de Koster, Wim C. de Leeuw, Benno H. ter Kuile, Gaurav Dugar

This study shows that overexpression of the Rob regulator in Yersinia enterocolitica accelerates antibiotic resistance development, but is costly without antibiotic selection.

Nucleic Acids Research · Jun 16, 2026Peer-reviewedMicrobiology

Driving factors for beta-lactam resistance gene amplification during de novo resistance evolution in E. coli

Luyuan Nong, Xinwei Liu, Xinyu Wang, Wim C. de Leeuw, Martijs J. Jonker, Stanley Brul, Benno H. ter Kuile

This study shows that ampC gene amplification drives beta-lactam resistance in E. coli, with resistance gene location affecting amplification targets but not the mechanism.

Antimicrobial Agents and Chemotherapy · Jul 23, 2025Peer-reviewedMicrobiology

Collateral sensitivity and cross resistance in six species of bacteria exposed to six classes of antibiotics

Xinyu Wang, Luyuan Nong, Gioia Schaar, Belinda B. Koenders, Martijs J. Jonker, Wim C. de Leeuw, Benno H. ter Kuile

The paper investigates collateral sensitivity and cross-resistance networks in six bacterial species after induced resistance to six antibiotics, finding specific patterns and genetic mechanisms.

Microbiology Spectrum · Jun 20, 2025Peer-reviewedMicrobiology

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Zhongyue Zhang, Zijie Qiu, Yingcheng Wu, Sitan Li, Dingyan Wang, Yong Liu, Zhuomin Zhou, Yusong Hu, Yuhan Chen, Duo An, Yongbo Wang, Haijun Yu, Zhenyi Zhong, Chubin Ou, Zichen Wang, , Shuangjia Zheng

OriGene identifies therapeutic targets by integrating diverse data modalities and outperforms human experts and models in accuracy and robustness.

bioRxiv · Jun 3, 2025 · PreprintBioinformatics