CHEN, Yiru

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Website version: 2026/04/05

BS @ Bioinformatics, ZJU-UoE 🇨🇳 🇬🇧

PhD @ Quantitative Biology and Medicine, Duke-NUS 🇸🇬 🇺🇸

Hi, I’m Yiru Chen.

Decoding biomedical complexity through the lens of AI and algorithms.

Download CV (PDF) PDF version: 2025.12.15 ORCID  ·  Google Scholar  ·  GitHub

Quick Background

I am currently completing my undergraduate training in Bioinformatics at the Zhejiang University-University of Edinburgh Institute (ZJU-UoE), Zhejiang University. In August 2026, I will join the Quantitative Biology and Medicine (QBM) Program at Duke-NUS Medical School as an incoming PhD student with a full scholarship.

My research interests center on spatial omics and representation learning. You can reach me at yiru.22@intl.zju.edu.cn or yiru2chen@gmail.com.

Short research statement

I develop algorithmic and statistical frameworks for spatial omics, computational immunology, and biomedical AI. My current work centers on multimodal integration, spatially resolved T-cell receptor analysis, simulation of spatial transcriptomics, and rigorous evaluation of computational methods. Across projects, I aim to turn mathematical modeling and machine learning into practical tools for decoding complex biological systems.

Publications

* Equal contribution. † Corresponding author.

Preprints

  1. From features to slice: parameter-cloud modeling of spatial transcriptomics for simulation and 3D interpolatory augmentation
    Yiru Chen*, Manfei Xie*, Yunfei Hu, Weiman Yuan, Hirak Sarkar, Bingshan Li, Lu Zhang†, and Xin Maizie Zhou†
    2026
    Independent first-author project; manuscript in final preparation
    PDF

Publications

2025

  1. A pan-disease and population-level single-cell TCRαβ repertoire reference
    Ziwei Xue*, Lize Wu*, Bing Gao*, Ruonan Tian, Yiru Chen, Yicheng Qi, Tianze Dong, Yadan Bai, Yu Zhao, Bing He, Lie Wang, Zuozhu Liu, Jianhua Yao, Linrong Lu†, and Wanlu Liu†
    Cell Discovery, 2025
  2. Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA
    Ruonan Tian*, Ziwei Xue*, Yiru Chen, Yicheng Qi, Jian Zhang, Jie Yuan, Dengfeng Ruan, Junxin Lin, Jia Liu, Di Wang, Youqiong Ye, and Wanlu Liu†
    Nature Communications, 2025

Manuscripts in Preparation, Under Review, or Forthcoming

Accepted / Forthcoming

  1. Integrative Inference of Spatially Resolved Cell Lineage Trees using LineageMap
    Xinhai Pan, Yiru Chen, and Xiuwei Zhang†
    Genome Research, 2026
    Accepted at RECOMB 2026; to appear in Genome Research

In Preparation / Under Review

  1. Recent advances in single-cell isoform profiling
    Zhejian Yu, Yanhui Chen, Yiru Chen, Yicheng Qi, and Wanlu Liu†
    Genomics, Proteomics & Bioinformatics, 2025
    Under review
  2. Mapping lineage-resolved scRNA-seq data with spatial transcriptomics using TemSOMap
    Xinhai Pan, Alejandro Danies-Lopez, Yiru Chen, and Xiuwei Zhang†
    2026
    Collaborative manuscript in final preparation

Presentations and Posters at Conferences

  1. SpatialTCR: An integrated platform for high-resolution spatial sequencing of T cell receptor repertoires
    Ruonan Tian*, Yiru Chen*, Yicheng Qi*, Ziwei Xue, Zhejian Yu, and Wanlu Liu†
    In GPB Omics and Bioinformatics Frontiers Symposium, 2025
    Co-first author; Presenting author
    Best Poster Award