CV

Education

• Ph.D. in Bioinformatics, University of Michigan, 2025
  • Advisor: Dr. Joshua Welch
• M.S. in Bioinformatics, University of Michigan, 2020
• B.S. in Biological Science, ShanghaiTech University, 2018

Work Experience

• May 2025 - Present: Postdoctoral Research Fellow
  • Howard Hughes Medical Institute & University of Michigan
  • Investigating lineage-guided neural wiring codes in the Drosophila brain
  • Advisors: Dr. Tzumin Lee and Dr. Tomer Stern
• January 2019 - May 2025: Ph.D. Candidate & Research Associate
  • University of Michigan
  • Developed CytoSignal, TopoVelo, and CytoSimplex for spatial transcriptomics
  • Identified bone marrow endosteal stem cells via single-cell multi-omic analysis
  • Advisor: Dr. Joshua Welch
• June 2017 - October 2017: Undergraduate Research Assistant
  • University of Oxford
  • Constructed transgenic Drosophila lines for prostate-like secondary cell studies
  • Advisor: Dr. Clive Wilson
• September 2016 - June 2018: Undergraduate Research Assistant
  • ShanghaiTech University
  • Studied enzyme compartmentation in budding and fission yeast
  • Advisor: Dr. Ji-Long Liu

Awards & Funding

• CZI Data Insights Cycle 2 (Co-PI, $397,108), Chan Zuckerberg Initiative, 2023
  • Detecting signaling among single cells from spatial transcriptomic data
• Rackham Predoctoral Fellowship, University of Michigan, 2023
• Dean’s Fellowship, ShanghaiTech University, 2014

Publications

First Author or Corresponding Author:

* Co-First author; # Co-Corresponding author

1. Liu, J., Manabe, H., Qian, W., Wang, Y., Gu, Y., Chu, A. K. Y., Gadhvi, G., Song, Y., Ono, N., Welch, J. D. “CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data”. Accepted at: Nature Genetics, 2026. DOI: 10.1101/2024.03.08.584153
2. Gu, Y.*, Liu, J.*, Lee, H. K., Li, C., Lu, L., Moline, J., Guan, R., Welch, J. D. “Topological Velocity Inference from Spatial Transcriptomic Data Maps Cell Fate Transition in Space and Time”. In: Nature Biotechnology, 1-12 (2025). DOI: 10.1038/s41587-025-02688-8
3. Liu, J.#, Wang, Y., Li, C., Gu, Y., Ono, N., Welch, J. D.# “CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex”. In: Bioinformatics (2025), btaf119. DOI: 10.1093/bioinformatics/btaf119
4. Gu, Y.*, Liu, J.*, Li, C., Welch, J. D. “Mapping Cell Fate Transition in Space and Time”. In: 28th International Conference on Research in Computational Molecular Biology (RECOMB), 2024. DOI: 10.1007/978-1-0716-3989-4_43
5. Matsushita, Y.*, Liu, J.*, Chu, A. K. Y., Tsutsumi-Arai, C., Nagata, M., Arai, Y., Ono, W., Yamamoto, K., Saunders, T. L., Welch, J. D., Ono, N. “Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis”. In: Nature Communications, 14.1 (2023), p. 2383. DOI: 10.1038/s41467-023-38034-2
6. Liu, J.*, Gao, C.*, Sodicoff, J., Kozareva, V., Macosko, E. Z., Welch, J. D. “Jointly defining cell types from multiple single-cell datasets using LIGER”. In: Nature Protocols, 15.11 (2020), pp. 3632-3662. DOI: 10.1038/s41596-020-0391-8

Contributing Author:

1. Zhang, H., Patrick, M. T., Zhao, J., Zhai, X., Liu, J., Li, Z., Gu, Y., Welch, J., Zhou, X., Modlin, R. L., Tsoi, L. C., Gudjonsson, J. E. “Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation”. In: Journal of Allergy and Clinical Immunology, 155.3 (2025), pp. 678-687. DOI: 10.1016/j.jaci.2025.01.009
2. Matsushita, Y., Liu, J., Chu, A. K. Y., Ono, W., Welch, J. D., Ono, N. “Endosteal stem cells at the bone-blood interface: A double-edged sword for rapid bone formation”. In: BioEssays, 46.3 (2023), p. 2300173. DOI: 10.1002/bies.202300173
3. Alghamri, M. S., McClellan, B. L., Avvari, R. P., Thalla, R., Carney, S., Hartlage, C. S., Haase, S., Ventosa, M., Taher, A., Kamran, N., Zhang, L., Faisal, S. M., Nunnez, F. J., Garcia-Fabiani, M. B., Al-Holou, W. N., Orringer, D., Hervey-Jumper, S., Heth, J., Patil, P. G., Eddy, K., Merajver, S. D., Ulintz, P. J., Welch, J. D., Gao, C., Liu, J., Nunez, G., Hambardzumyan, D., Lowenstein, P. R., Castro, M. G. “G-CSF secreted by mutant IDH1 glioma stem cells abolishes myeloid cell immunosuppression and enhances the efficacy of immunotherapy”. In: Science Advances, 7.40 (2021), eabh3243. DOI: 10.1126/sciadv.abh3243
4. Gao, C., Liu, J., Kriebel, A. R., Preissl, S., Luo, C., Castanon, R., Sandoval, J., Rivkin, A., Nery, J. R., Behrens, M. M., Ecker, J. R., Ren, B., Welch, J. D. “Iterative single-cell multi-omic integration using online learning”. In: Nature Biotechnology, 39.8 (2021), pp. 1000-1007. DOI: 10.1038/s41587-021-00867-x

Teaching

MCDB 421 — Single-Cell Data Integration

Professional Service

• Peer review: RECOMB, IEEE TCBB, BMC Bioinformatics, npj Artificial Intelligence, BioEssays