Publications

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

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

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

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

   Best Poster Award