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.
Monkey D. Luffy, Ph.D.
Computational biologist moving from single-cell and spatial multi-omics into connectome-scale neuroscience.
Boston, MA/
(555) 019-2847/
monkeyd.luffy@example.com/
Google Scholar/
monkeydluffy.example.com/cv
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
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 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.
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 across 6 organs): milestone tracking, multi-site QC, multi-PI coordination.
Selected Publications
01Reyes M*, Luffy MD*, 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.
02Luffy MD*, 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.
03Luffy MD*, Delgado J*, Moreau S, et al. "Deciphering Dysfunctional Regulatory T Cells in Vitiligo." Allergy IF 12.6 · 2025.
04Alvarez J*, Luffy MD*, 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.
05Novak L*, Luffy MD*, 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.
06Luffy MD*, 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)2024
Immunosuppression Composition with 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.
Professor, HNU College of Medicine; CEO/CSO, Meridian Immune. Ph.D. advisor.
mhsuh@hangang.ac.krJi-Won Baek, M.D., Ph.D.
Assistant Professor, HNU, Microbiology & Immunology / IBRI. Computational co-corresponding.
jwbaek@hangang.ac.krDae-Ho Yoon, Ph.D.
Professor, Nakdong Wonju, Physiology. Most recent research supervisor.
dhyoon@nakdong.ac.kr