Publications

1. 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

2026

1. Integrative Inference of Spatially Informed Cell Lineage Trees using LineageMap

   Xinhai Pan, Yiru Chen, and Xiuwei Zhang

   In RECOMB 2026 Proceedings, 2026

   HTML

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

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 & Bioinformatics Frontiers Symposium, 2025

   Yiru Chen (presenter)

   Best Poster Presentation Award

   Best Poster Presentation Award