Hello,

I am Ruonan Tian

I'm a PhD student in Bioinformatics at Zhejiang University, specializing in multi-omics data analysis and computational framework development.

Ruonan Tian

Research Interests

My research focuses on developing computational methods and analytical frameworks for spatial multi-omics data. During my PhD, I have been working on integrative approaches for cross-sample and cross-modal integration of spatial transcriptomics and spatial metabolomics, as well as the development of single-cell TCR sequencing methods. I have also applied multi-omics approaches to the study of intestinal tissues, aiming to better understand tissue organization and immune heterogeneity.

I am particularly interested in tackling the challenges of high-dimensional and heterogeneous biological data by designing novel computational methods (including machine learning and statistical modeling) that can extract meaningful biological insights and improve the analysis of omics datasets.

Looking forward, my research interests lie in developing AI-driven computational frameworks for multi-omics integration and constructing large-scale, high-resolution cellular and molecular atlases across tissues and disease contexts.

Publications

Highlighted publications

  • Tian, R.*, Chen, Y., Qi, Y., Xue, Z., Liu, W.#. ScSpaTCR: An Integrated Platform for Single-Cell Resolution Spatial Sequencing of T Cell Receptor Repertoires. (In preparation)
  • Tian, R.*, Xue, Z.*, Chen, Y ., Qi, Y ., Zhang, J., Yuan, J., Ruan, D., Lin, J., Liu, J., Wang, D., Ye, Y ., Liu, W.#. Integrating Cross-Sample and Cross-Modal Data for Spatial Transcriptomics and Metabolomics with SpatialMETA.Nature Communications, 2025
  • Tian, R.*, Yu, Z.*, Xue, Z., Wu, J., Wu, L., Cai, S., Gao, B., He, B., Zhao, Y ., Yao, J., Lu, L., Liu, W.#. Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data. Genomics, Proteomics & Bioinformatics, 2024
  • Tian, R.*, Xue, Z.*, Ruan, D.*, Chen, P ., Xu, Y ., Dai, C., Shen, W., Ouyang, H.#, Liu, W.#, Lin, J.#. MSdb: an integrated expression atlas of human musculoskeletal system. iScience, 2023
  • Zhang, J.*, Tian, R.* , Liu, J.*, Yuan, J.*, Zhang, S., Chi, Z., Yu, W., Yu, Q., Wang, Z., Chen, S., Li, M., Yang, D., Hu, T ., Deng, Q., Lu, X., Yang, Y ., Zhou, R., Zhang, X., Liu, W.#, Wang, D.#. A two-front nutrient supply environment fuels the physiology of the small intestine through differential regulation of nutrient absorption and host defense. Cell, 2024
  • Ruan, D.*, Tian, R.* , Li, Z., Yin, L., Tian, W., Chen, X., Xu, Y ., Meng, Q., Zhou, W., Liu, H., Cai, H., Wang, X., Luo, Q., Lin, J.#, Liu, W.#, Shen, W.#. A Multi-Omics Atlas of Human MSCs Reveals Therapeutic Heterogeneity across Tissues and Clones. Cell Stem Cell (Under review)

Other publications

  • Chen, Y .*, Yan, Y .*, Tian, R., Sheng, Z., Li, L., Chen, J., Liao, Y., Wen, Y., Lu, J., Liu, X., Sun, W., Wu, H., Liao, Y., Zhang, X., Chen, X., An, C., Zhao, K., Liu, W., Gao, J., Hay, D. C., Ouyang, H.#. Chemically programmed metabolism drives a superior cell fitness for cartilage regeneration. Science Advances, 2024
  • Xue, Z.*, Wu, L.*, Tian, R., Gao, B., Zhao, Y., He, B., Sun, D., Zhao, B., Li, Y., Zhu, K., Wang, L., Yao, J.#, Liu, W.#, Lu, L.#. Integrative mapping of human CD8+ T cells in inflammation and cancer. Nature Methods, 2024
  • Xue, Z.*, Wu, L.*, Gao, B.*, Tian, R., Chen, Y., Qi, Y., Dong, T., Liu, Z., Bai, Y., Sun, D., Guo, Y., Chen, P., Zhao, Y., He, B., Wang, L., Yao, J., Lu, L.#, Liu, W.#. Disease associated human TCR characterization by deep-learning framework TCR.Deepinsight: A pan-disease single-cell TCRαβ repertoire reference atlas. Cell Discovery, 2025
  • Xiang, Y .*, Qian, Y .*, Li, Z.*, Wang, J*, Tian, R., Meng, W., Bu, J., Huang, F., Ai, Z., Wu, D., Chen, X., Wu, Y., Shen, L., Chan, Y.-S., Gao, Y., Ma, J., Liu, W.#, Gao, S.#, Zhang, D.#, Liang, H.#. Endogenous retroviruses synthesize heterologous chimeric RNAs to reinforce human early embryonic development. Science, 2026

Education

  • Sep 2023 - Present

    Ph.D. student in Bioinformatics

    ZJU-UoE Institute, Zhejiang University (Supervisor: Dr. Wanlu Liu)

  • Sep 2021 - Jun 2023

    Master student in Bioinformatics

    Zhejiang University (Supervisor: Dr. Wanlu Liu)

  • Sep 2017 - Jun 2021

    Bachelor in Bioinformatics

    Huazhong Agricultural University (GPA: 3.76/4.00)

Awards & Scholarships

Skills

Programming

Python (NumPy, Pandas, Django, PyTorch, Scanpy), R (Seurat, ggplot2), HTML/CSS, JavaScript, SQL

Dry Lab / Analysis

Spatial multi-omics, scRNA-seq, scTCR-seq, Hi-C, ChIP-seq, ATAC-seq, RNA-seq; algorithm development; web development

Wet Lab

T/B cell isolation, molecular cloning, ATAC-seq library prep, spatial TCR library

Miscellaneous

Linux, Git, Adobe Illustrator, Microsoft Office, LaTeX

Software & Database

MSdb

An integrated expression atlas of the human musculoskeletal system.

SpatialMETA

An open framework for integrating spatial transcriptomics and spatial metabolomics.

Conferences & Presentations

Reviewer

Contact

Address: 718 East Haizhou Rd. Haining, Zhejiang 314400, P.R. China

Email: ruonan.23@intl.zju.edu.cn

GitHub: Ruonan Tian

Google Scholar: Google Scholar