Ph.D., Biomedical Sciences
Hangang National University · Seoul, Republic of Korea
Thesis: Mapping Dendritic Cell Heterogeneity Across Chronic Inflammatory Contexts · Advisor: Min-Ho Suh, M.D., Ph.D.
2014–2023
Postdoctoral applicant · single-cell / spatial multi-omics · ML/DL
James T. Kirk존 도, Ph.D.
Computational biologist moving from single-cell and spatial multi-omics into connectome-scale neuroscience.
LOCBoston, MA 02135
TEL(555) 019-2847
EMLjamest.kirk@example.com
WEBjamestkirk.example.com/cv
01Profile
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.
02Education
M.S., Biomedical Sciences
Hangang National University · Seoul
Thesis: Enhanced LPS-Induced Monocyte Activation by Recombinant Human Soluble CD180
2012–2014
B.S., Genetic Engineering
Suwon Institute of Life Sciences · Suwon
2008–2012
03Experience
Postdoctoral Researcher
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.
2025–2026
Associate Director
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/MS multi-omic studies; oversaw regulatory documentation for an anti-CD25 humanized-antibody program.
2023–2025
Researcher
Xenotransplantation Research Center, HNU · Seoul
Rhesus macaque tissue processing, longitudinal immune monitoring, CNS (brain/spinal cord) tissue handling.
2019–2021
Research Student · MOSAIC
Multi-Organ Single-cell Atlas of Immune Cells, Genomic Medicine Institute, HNU
Contributed the founding proposal; executed within the funded program (500+ donors × 6 organs): milestone tracking, multi-site QC, multi-PI coordination.
2020–2023
04Selected Publications
01Reyes 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). Custom UMI-aware BAM-level isoform analysis; scRNA + scTCR + snATAC integration; ML classifier AUC 0.812; 702 samples, 251,055 memory CD4⁺ T cells.
02Kirk 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.
03Kirk JT*, Delgado J*, Moreau S, et al. "Deciphering Dysfunctional Regulatory T Cells in Vitiligo." Allergy IF 12.6 · 2025.
04Alvarez J*, Kirk JT*, et al. "Long-term control of diabetes by a baricitinib-based regimen after allo-islet transplantation in diabetic rhesus monkeys." Xenotransplantation IF 3.9 · 2024.
05Novak L*, Kirk JT*, et al. "Intra-tumoral heterogeneity and immune escape of melanoma arising from chronic UV photodamage by spatial gene expression profiling." JEADV IF 9.2 · 2022.
06Kirk JT*, 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).
05Technical 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 (domain ground truth). 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.
06Awards, Patents & Scholarships
Antagonistic Anti-CD25 Humanized Antibody · Patent 10202400918452024
Immunosuppression Composition w/ PI3K Inhibitor · Patent 10201434962172019
Grand Prize, AI Builders Hackathon (Project Nova Team)2024
Grand Prize, Metro Innovation Workathon (Work Process Innovation)2023
Best Poster, American Transplant Congress (Chicago)2017
NRF Ph.D. Scholarship · BK21 Plus · HNU Dean's Support2014–2020
07References
Min-Ho Suh, M.D., Ph.D.
Professor, HNU College of Medicine; CEO/CSO, Meridian Immune Therapeutics. Ph.D. advisor.
mhsuh@hangang.ac.krJi-Won Baek, M.D., Ph.D.
Assistant Professor, Microbiology & Immunology / IBRI, HNU. Computational co-corresponding.
jwbaek@hangang.ac.krDae-Ho Yoon, Ph.D.
Professor, Physiology & Global Medical Science, Nakdong Wonju. Recent research supervisor.
dhyoon@nakdong.ac.kr