Naruto Uzumaki, Ph.D.
Computational Single-Cell Scientist · Single-Cell / Spatial Multi-Omics · ML/DL
Boston, MA 02135|(555) 019-2847|naruto.uzumaki@example.com
Google Scholar|narutouzumaki.example.com/cv

Summary

Moving from wet-lab immunology into computational neuroscience. I build methods that infer cellular identity, state, and interaction from large, incomplete single-cell and spatial data. Research objective: connect molecular cell identity to circuit structure and function by integrating connectomics with transcriptomics, growing into connectome-constrained circuit models.

Education

Ph.D., Biomedical Sciences2014–2023
Hangang National University · Seoul, Republic of Korea
Thesis: Mapping Dendritic Cell Heterogeneity Across Chronic Inflammatory Contexts. Advisor: Min-Ho Suh, M.D., Ph.D.
M.S., Biomedical Sciences2012–2014
Hangang National University · Seoul
Thesis: Enhanced LPS-Induced Monocyte Activation by Recombinant Human Soluble CD180.
B.S., Genetic Engineering2008–2012
Suwon Institute of Life Sciences · Suwon

Professional Experience

Postdoctoral Researcher2025–2026
Nakdong University Wonju College of Medicine · Physiology / Cellular Systems Research Center
  • Developed deep-learning multimodal-integration models fusing imaging, transcriptomic, and clinical data into single predictive models.
Associate Director2023–2025
Meridian Immune Therapeutics Inc. · Basic Research, Seoul
  • Built in-house single-cell and spatial transcriptomics analysis code from scratch.
  • Led cross-functional NHP (cynomolgus, marmoset) EAE/multiple-sclerosis multi-omic studies.
  • Oversaw regulatory documentation for an anti-CD25 humanized-antibody program.
Researcher2019–2021
Xenotransplantation Research Center, HNU · Seoul
  • Rhesus macaque tissue processing, longitudinal immune monitoring, CNS (brain/spinal cord) tissue handling.
Research Student2020–2023
MOSAIC, Multi-Organ Single-cell Atlas of Immune Cells, HNU · Genomic Medicine Institute
  • Contributed the founding proposal; executed within the funded program (500+ donors across 6 organs): milestone tracking, multi-site QC, multi-PI coordination.

Selected Publications

18 total papers | 17 peer-reviewed | 6 first / co-first | 1 under review. Co-first denotes equal contribution.
1.Reyes M*, Uzumaki N*, Alvarez T*, et al. "Conserved PDE9X short-isoform bias defines pathogenic Th1.17 state across human inflammatory diseases." Nature Immunology IF 27.7 · under review (2026). Custom UMI-aware BAM-level isoform analysis (Python); consensus NMF; scRNA + scTCR + snATAC integration; disease-state ML classifier (AUC 0.812); 588 samples, 19 diseases, 214,300 memory CD4⁺ T cells.
2.Uzumaki N*, Tanaka Y*, Truong P*, et al. "Immune cell-enriched scRNA-seq unveils the interplay between infiltrated CD8⁺ T resident memory cells and meningeal lymphatic endothelial cells in Parkinson's disease." Journal of Neuroimmunology IF 2.9 · 2025. 9,240 cells, 8 immune populations.
3.Uzumaki N*, Delgado J*, Moreau S, et al. "Deciphering Dysfunctional Regulatory T Cells in Vitiligo." Allergy IF 12.6 · 2025.
4.Alvarez J*, Uzumaki N*, et al. "Long-term control of diabetes by baricitinib-based immunosuppressive regimen after allo-islet transplantation in diabetic rhesus monkeys." Xenotransplantation IF 3.9 · 2024.
5.Novak L*, Uzumaki N*, et al. "Intra-tumoral heterogeneity and immune escape of melanoma arising from chronic UV photodamage revealed by spatial gene expression profiling." JEADV IF 9.2 · 2022.
6.Uzumaki N*, et al. "mTOR inhibitor-based immunosuppression in allogeneic islet transplantation." Islets IF 2.2 · 2019.
Co-author (selected): eBioMedicine (IF 11.1, 2024); JEADV (IF 9.2, 2024); Current Diabetes Reports (IF 4.2, 2021).

Technical Skills

Single-cell / spatial / multi-omic: scRNA-seq, scTCR-seq, snRNA/snATAC; Seurat, Scanpy, Squidpy, Monocle3, CellChat/NicheNet; scVI/scANVI, batch integration, consensus NMF, embedding geometry; custom UMI-aware BAM-level isoform code (Python); Milo KNN-graph DA, GLIPH, Shannon-entropy clonality, InferCNV, weighted-LMM/EMM; GeoMx DSP (WTA + TCR); Olink targeted plasma proteomics.
Machine learning / deep learning / AI: Python (scikit-learn, XGBoost/LightGBM/CatBoost, PyTorch); AUC-validated classifiers; VAE/GAN/GNN; multimodal DL integration (imaging + transcriptomic + clinical); vision-language transformers; AlphaFold2/3, ProteinMPNN, DiffDock, MolFormer; Linux servers, R/RStudio, Git-based reproducible analysis.
Experimental: 10x 5′/3′ scRNA + scTCR library generation; high-dimensional flow cytometry (up to 24 markers), 10-color 6-way FACS; brain/CNS immune profiling (perfusion, digestion, Percoll, CD45⁺ FACS); IHC/IF (frozen and FFPE); two-photon microscopy; NHP CNS tissue (rhesus, cynomolgus, marmoset); EAE/MS and islet-transplant disease models.

Awards, Patents & Scholarships

Antagonistic Anti-CD25 Humanized Antibody. Patent No. 1020240091845 (registered 2024-07-01).2024
Immunosuppression Composition Comprising PI3K Inhibitor. Patent No. 1020143496217 (registered 2019-08-20).2019
Grand Prize, 2024 AI Builders Hackathon (Project Nova Team).2024
Grand Prize, Metro Innovation Workathon (Work Process Innovation).2023
Best Poster, American Transplant Congress, Chicago; Best Presentation, Korean Association of Immunologists.2017
NRF Ph.D. Research Scholarship; HNU Dean's Lecture & Research Support; BK21 Plus Research Scholarship.2014–2020

References

Min-Ho Suh, M.D., Ph.D.
Professor, HNU College of Medicine; CEO/CSO, Meridian Immune. Ph.D. advisor.
mhsuh@hangang.ac.kr
Ji-Won Baek, M.D., Ph.D.
Assistant Professor, HNU, Microbiology & Immunology / IBRI. Computational co-corresponding.
jwbaek@hangang.ac.kr
Dae-Ho Yoon, Ph.D.
Professor, Nakdong Wonju, Physiology. Most recent research supervisor.
dhyoon@nakdong.ac.kr