CHEN, Yiru

Yiru's Version: 2026/08/05

BS @ Bioinformatics, ZJU-UoE 🇨🇳 🇬🇧

PhD Student @ 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: 2026.08.05 ORCID · Google Scholar · GitHub

Quick Background

I am a PhD student in the Quantitative Biology and Medicine (QBM) Programme at Duke-NUS Medical School, Singapore. My undergraduate training in Bioinformatics was at the Zhejiang University-University of Edinburgh Institute (ZJU-UoE), Zhejiang University.

My research interests center on spatial omics and computational immunology, with a general interest in AI for biomedicine. You can reach me at yiru_chen@u.duke.nus.edu 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

From Parameter Clouds to Virtual Slices: Layout-Aware Simulation and Benchmark Construction for Spatial Transcriptomics

Yiru Chen^†, Manfei Xie^†, Yunfei Hu, Weiman Yuan, Hirak Sarkar, Bingshan Li, Lu Zhang^*, and Xin Maizie Zhou^*

Preprint, 2025

Publications

2026

Integrative Inference of Spatially Informed Cell Lineage Trees using LineageMap

Xinhai Pan, Yiru Chen, and Xiuwei Zhang

In RECOMB 2026 Proceedings, 2026

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2025

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
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

Presentations and Posters at Conferences

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 & Bioinformatics Frontiers Symposium, 2025

Yiru Chen (presenter)

Best Poster Presentation Award

Best Poster Presentation Award