Ph.D., Biomedical Sciences
2014–2023
Hangang National University · Seoul, Republic of Korea
Thesis: Mapping Dendritic Cell Heterogeneity Across Chronic Inflammatory Contexts. Advisor: Min-Ho Suh, M.D., Ph.D.
James T. Kirk, Ph.D.
Computational biologist, single-cell & spatial multi-omics toward connectome-scale neuroscience
Profile
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
M.S., Biomedical Sciences
2012–2014
Hangang National University · Seoul
Thesis: Enhanced LPS-Induced Monocyte Activation by Recombinant Human Soluble CD180.
B.S., Genetic Engineering
2008–2012
Suwon Institute of Life Sciences · Suwon
Research & Professional Experience
Postdoctoral Researcher
2025–2026
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 Director
2023–2025
Meridian Immune Therapeutics Inc. · Basic Research, Seoul
Built in-house single-cell & spatial transcriptomics analysis code from scratch; led cross-functional NHP (cynomolgus, marmoset) EAE/MS multi-omic studies; oversaw regulatory documentation for an anti-CD25 humanized-antibody program.
Researcher
2019–2021
Xenotransplantation Research Center, HNU · Seoul
Rhesus macaque tissue processing, longitudinal immune monitoring, CNS (brain/spinal cord) tissue handling.
Research Student
2020–2023
MOSAIC, Multi-Organ Single-cell Atlas of Immune Cells, HNU · Genomic Medicine Institute
Contributed the founding proposal; executed within the funded program (500+ donors × 6 organs): milestone tracking, multi-site QC, multi-PI coordination.
Selected Publications
- Reyes M*, Kirk JT*, 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. UMI-aware BAM-level isoform analysis; scRNA + scTCR + snATAC integration; ML classifier AUC 0.812; 702 samples, 251,055 CD4⁺ T cells.
- Kirk JT*, Tanaka Y*, Truong P*, et al. Immune cell-enriched scRNA-seq unveils infiltrated CD8⁺ T resident memory cells and meningeal lymphatic endothelium in Parkinson's disease. Journal of Neuroimmunology, IF 2.9, 2025. 9,240 cells, 8 immune populations.
- Kirk JT*, Delgado J*, Moreau S, et al. Deciphering Dysfunctional Regulatory T Cells in Vitiligo. Allergy, IF 12.6, 2025.
- Alvarez J*, Kirk JT*, et al. Long-term control of diabetes by a baricitinib-based regimen after allo-islet transplantation in rhesus monkeys. Xenotransplantation, IF 3.9, 2024.
- Novak L*, Kirk JT*, et al. Intra-tumoral heterogeneity and immune escape of melanoma from chronic UV photodamage by spatial gene expression profiling. JEADV, IF 9.2, 2022.
- Kirk JT*, et al. mTOR inhibitor-based immunosuppression in allogeneic islet transplantation. Islets, IF 2.2, 2019.
Selected co-authorships: 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; custom UMI-aware BAM-level isoform code (Python); Milo, GLIPH, InferCNV, weighted-LMM; GeoMx DSP; Olink proteomics.
Machine learning / deep learning / AI. Python (scikit-learn, XGBoost/LightGBM/CatBoost, PyTorch); AUC-validated classifiers; VAE/GAN/GNN; multimodal DL (imaging + transcriptomic + clinical); AlphaFold2/3, ProteinMPNN, DiffDock, MolFormer; Linux, R, Git-based reproducible analysis.
Experimental. 10x 5′/3′ scRNA + scTCR libraries; high-dimensional flow cytometry (24 markers); brain/CNS immune profiling; IHC/IF; two-photon microscopy; NHP CNS tissue (rhesus, cynomolgus, marmoset); EAE/MS & islet-transplant models.
Awards, Patents & Scholarships
Antagonistic Anti-CD25 Humanized Antibody (Patent)2024
Immunosuppression Composition w/ PI3K Inhibitor (Patent)2019
Grand Prize, AI Builders Hackathon (Project Nova)2024
Grand Prize, Metro Innovation Workathon2023
Best Poster, American Transplant Congress, Chicago2017
NRF Ph.D. Scholarship · BK21 Plus · HNU Dean's2014–2020
References
Min-Ho Suh, M.D., Ph.D.
HNU College of Medicine; CEO/CSO, Meridian Immune. Ph.D. advisor.
mhsuh@hangang.ac.krJi-Won Baek, M.D., Ph.D.
HNU, Microbiology & Immunology / IBRI. Computational co-corresponding.
jwbaek@hangang.ac.kr