publications

2026

1. PSB

   Mapping lineage-resolved scRNA-seq data with spatial transcriptomics using TemSOMap

   Xinhai Pan, Alejandro Danies-Lopez, Yiru Chen, and 1 more author

   In Pacific Symposium on Biocomputing, 2026

   Bib

   @inproceedings{pan2026temsomap,
     title = {Mapping lineage-resolved scRNA-seq data with spatial transcriptomics using TemSOMap},
     author = {Pan, Xinhai and Danies-Lopez, Alejandro and Chen, Yiru and Zhang, Xiuwei},
     booktitle = {Pacific Symposium on Biocomputing},
     year = {2026},
     status = {Submitted},
   }

2025

1. Cell Discov

   A pan-disease and population-level single-cell TCR repertoire reference

   Ziwei Xue, Lize Wu, Bing Gao, and 12 more authors

   Cell Discovery, 2025

   Bib

   @article{xue2025pancancer,
     title = {A pan-disease and population-level single-cell TCR repertoire reference},
     author = {Xue, Ziwei and Wu, Lize and Gao, Bing and Tian, Ruonan and Chen, Yiru and Qi, Yicheng and Dong, Tianze and Bai, Yadan and Zhao, Yu and He, Bing and Wang, Lie and Liu, Zuozhu and Yao, Jianhua and Lu, Linrong and Liu, Wanlu},
     journal = {Cell Discovery},
     year = {2025},
     status = {Accepted},
   }

2. Nat Commun

   Integrating Cross-Sample and Cross-Modal Data for Spatial Transcriptomics and Metabolomics with SpatialMETA

   Ruonan Tian, Ziwei Xue, Yiru Chen, and 9 more authors

   Nature Communications, 2025

   Bib

   @article{tian2025spatialmeta,
     title = {Integrating Cross-Sample and Cross-Modal Data for Spatial Transcriptomics and Metabolomics with SpatialMETA},
     author = {Tian, Ruonan and Xue, Ziwei and Chen, Yiru and Qi, Yicheng and Zhang, Jian and Yuan, Jie and Ruan, Dengfeng and Lin, Junxin and Liu, Jia and Wang, Di and Ye, Youqiong and Liu, Wanlu},
     journal = {Nature Communications},
     year = {2025},
     status = {Accepted},
   }

3. GPB

   Recent Advances in Single-Cell Isoform Profiling

   Zhejian Yu, Yanhui Chen, Yiru Chen, and 2 more authors

   Genomics, Proteomics & Bioinformatics, 2025

   Bib

   @article{yu2025isoform,
     title = {Recent Advances in Single-Cell Isoform Profiling},
     author = {Yu, Zhejian and Chen, Yanhui and Chen, Yiru and Qi, Yicheng and Liu, Wanlu},
     journal = {Genomics, Proteomics & Bioinformatics},
     year = {2025},
     status = {Under Review},
   }

4. GPB Symp

   SpatialTCR: An integrated platform for high-resolution spatial sequencing of T cell receptor repertoires

   Ruonan Tian, Yiru Chen, Yicheng Qi, and 3 more authors

   In GPB Omics and Bioinformatics Frontiers Symposium, 2025

   Co-first author, Presenting author

   Bib

   @inproceedings{chen2025spatialtcr,
     title = {SpatialTCR: An integrated platform for high-resolution spatial sequencing of T cell receptor repertoires},
     author = {Tian, Ruonan and Chen, Yiru and Qi, Yicheng and Xue, Ziwei and Yu, Zhejian and Liu, Wanlu},
     booktitle = {GPB Omics and Bioinformatics Frontiers Symposium},
     year = {2025},
     status = {Best Poster Award},
     note = {Co-first author, Presenting author}
   }