Ziwei Xue

Major in Bioinformatics, ZJU-UoE Institute, Zhejiang University 📧 ziwei.21@intl.zju.edu.cn

Find my CV here

About

I am a PhD student major in bioinformatics in Zhejiang University - University of Edinburgh (ZJU-UoE) institute. I am interested in multi-omics data analysis, focusing on developing machine-learning and deep-learning methods to gain deeper insights into the phenotypic diversity of immune cells in cancer and autoimmune diseases. My research centers on integrating the growing volume and diversity of next generation sequencing data across multiple modalities, including genomics, transcriptomics, proteomics, and immunomics, at bulk, single cell, and spatial resolutions, to provide a comprehensive view of immune system dynamics in disease contexts.

Education Experience

2021 - Present

PhD Student major in Bioinformatics, ZJE institute, Zhejiang University

2017 - 2021

Bachelor major in Biomedical science, ZJE institute, Zhejiang University

2014 - 2017

Shenzhen Middle School

Publications

  1. Patterns journal logo

    DestinyNet: A deep learning framework integrating lineage tracing and single-cell sequencing information for fate clustering, flow, and prediction

    Liu, Z.*, Jiang, S.*, Hu, T.*, Xue, Z.*, Chen, Y., Ruan, D., Xia, H., Feng, Y., Hao, J., Li, W., Zhou, T., Fang, B., Wu, J., Liu, W.# (2025) Patterns, 7, 101471.

    DestinyNet is a multi-task deep-learning framework for lineage-tracing single-cell RNA-seq data that supports fate clustering, fate flow, and fate prediction across diverse datasets.
  2. Cell Discovery journal logo

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

    Xue, Z., Wu, L., Gao, B., Tian, R., Chen, Y., Qi, Y., Dong, T., Bai, Y., Zhao, Y., He, B., Wang, L., Liu, Z., Yao, J., Lu, L.#, Liu, W.# (2025) Cell Discovery, 11, 82.

    Comprehensive single-cell T cell receptor (TCR) repertoire analysis across diseases and populations, enabling deeper understanding of immune cell diversity and function.
  3. Nature Communications journal logo

    Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA

    Tian, R., Xue, Z., Chen, Y., Qi, Y., Zhang, J., Yuan, J., Ruan, D., Lin, J., Liu, J., Wang, D., Ye, Y., & Liu, W.# (2025) Nature Communications, 16, 8855.

    A comprehensive framework for integrating spatial transcriptomics and metabolomics data across multiple samples and modalities, advancing multi-omics analysis.
  4. Nature Reviews Cancer journal logo

    scAtlasVAE: a deep learning framework for generating a human CD8+ T cell atlas

    Xue, Z. (2025) Nature Reviews Cancer, 25, 319.

    A deep learning approach for constructing comprehensive human CD8+ T cell atlases from single-cell data, enabling systematic characterization of T cell diversity and function.
  5. GPB journal logo

    Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data

    Tian, R.*, Yu, Z.*, Xue, Z., Wu, J., Wu, L., Cai, S., Gao, B., He, B., Zhao, Y., Yao, J., Lu, L., Liu, W.# (2025) Genomics, Proteomics & Bioinformatics, 22, qzae086.

    A comprehensive evaluation of different computational methods for reconstructing T cell receptor sequences from single-cell RNA sequencing data.
  6. Nature Methods journal logo

    Integrative mapping of human CD8+ T cells in inflammation and cancer

    Xue, Z.*, Wu, L.*, Tian, R., Gao, B., Zhao, Y., Bing, H., Zhao, B., Li, Y., Zhu, K., Wang, L., Yao, J.#, Liu, W.# & Lu, L.# (2025) Nature Methods, 22, 435-445.

    A comprehensive integrative analysis mapping human CD8+ T cell states across inflammatory and cancerous contexts using multi-modal single-cell data.
  7. Mobile DNA journal logo

    CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements

    Guo, Y.*, Xue, Z., Gong, M., Jin, S., Wu, X. & Liu, W.# (2024) Mobile DNA, 15, 3.

    A web-based platform for designing CRISPR guide RNAs specifically targeting transposable elements, facilitating functional genomics studies.
  8. Nature Communications journal logo

    Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data

    Su, Y.*, Yu, Z., Jin, S., Ai, Z., Yuan, R., Chen, X., Xue, Z., Guo, Y., Chen, D., Liang, H., Liu, Z., Liu, W. (2024) Nature Communications, 15, 3972.

    A systematic evaluation of computational methods for detecting mRNA isoforms using long-read sequencing technologies.
  9. iScience journal logo

    MSdb: An integrated expression atlas of human musculoskeletal system

    Tian, R.*, Xue, Z.*, Ruan, D., Chen, P., Xu, Y., Dai, C., Shen, W., Ouyang, H., Liu, W., and Lin, J. (2023) iScience, 26, 106933.

    A comprehensive expression atlas of the human musculoskeletal system combining multi-tissue and multi-cell type transcriptomic data.
  10. Nature Communications journal logo

    Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network

    Li, Z., Xu, H., Li, J., Xu, X., Wang, J., Wu, D., Zhang, J., Liu, J., Xue, Z., Zhan, G., Tan, B.C.P., Chen, D., Chan, Y-S., Ng, H.H., Liu, W., Hsu, C-H., Zhang, D., Shen, Y. & Liang, H. (2023) Nature Communications, 14, 3646.

    A study revealing the role of ZFP352 in regulating retrotransposons during the transition from totipotency to differentiation.
  11. NAR journal logo

    huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level

    Wu, L.*, Xue, Z.*, Jin, S., Zhang, J., Bai, Y., Jin, X., Wang, C., Wang, L., Wang, J.Q., Lu, L. & Liu, W.# (2022) Nucleic Acids Research, 50(D1), D1244-D1254.

    A comprehensive database integrating T/B cell receptor sequences with transcriptomic data, enabling joint analysis of immune receptor clonotypes and gene expression.
  12. Nature Communications journal logo

    Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections

    Xiang, X.*, Tao, Y., DiRusso, J., Hsu, F.-M., Zhang, J., Xue, Z., Pontis, J., Trono, D., Liu, W., and Clark, A.T. (2022) Nature Communications, 13, 463.

    Discovery of the regulatory role of ancient retrotransposons in human embryonic development and reproduction.
  13. BBRC journal logo

    Identification of SRSF3 target mRNAs using inducible TRIBE

    Jin, S.*, Xue, Z.*, Zhang, J., Wang, Z., Zhang, J., Chen, D.#, Liu, W.#, Lin, J.# (2021) Biochemical and Biophysical Research Communications, 578, 21-27.

    Application of TRIBE technology to systematically identify mRNA targets of the splicing regulator SRSF3.
  14. Bioinformatics journal logo

    RAD: a web application to identify region associated differentially expressed genes

    Guo, Y.*, Xue, Z., Yuan, R., Li, J., Pastor, W. & Liu, W.# (2021) Bioinformatics, 37, 2741-2743.

    A web-based tool for identifying spatially and temporally relevant differentially expressed genes from genomic region analysis.
*, first or co-first author; #, corresponding author.


Code on Github and full publication list on Google Scholar!

Talks and Presentations

14th National Conference on Bioinformatics and Systems Biology, Nanning, China — Oct 7–10, 2025 Oct 2025

Invited talk: AI-Driven Integration of Single-Cell Immunomics Reveals T Cell Phenotypic Plasticity and TCR Diversity

Annual Meeting of American Association of Immunology (AAAI) May 2025

Poster: Unified integration of pan-cancer single-cell and spatial transcriptomics

Human Cell Atlas Asia Meeting Dec 2024

Poster: Integrative Mapping of Human CD8+ T Cell in Inflammation and Cancer

Poster: A pan-disease and population-level single-cell TCRαβ repertoire reference atlas

Honors

2025

Chu Kochen Scholarship of Zhejiang University (竺可桢奖学金)

2025

National Scholarship of China (国家奖学金)

2025

Student of Distinction of the International Campus (国际校区先锋学子)

2024

Qiu Shi Rising Star Ph.D. student Scholarship of Zhejiang University (求是新星培养计划)

2022, 2023, 2024, 2025

Excellent Graduate Student of Zhejiang University (浙江大学优秀研究生)

2022

Academic Poster Exhibition, College of Medicine, Zhejiang University (浙江大学医学院学术墙报展)

2022

1st Interdisciplinary Innovation Competition, International Campus, Zhejiang University (浙江大学国际校区第一届交叉创新大赛)


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