Ph.D., Biomedical Sciences
2014–2023
Hangang National University, Seoul
Thesis: Mapping Dendritic Cell Heterogeneity Across Chronic Inflammatory Contexts. Advisor: Min-Ho Suh, M.D., Ph.D.
Thomas Shelby, Ph.D.
Computational biologist moving from single-cell and spatial multi-omics into connectome-scale neuroscience
addr Boston, MA 02135
tel (555) 019-2847
mail thomas.shelby@example.com
web Google Scholar
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
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 code from scratch; led NHP (cynomolgus, marmoset) EAE/MS multi-omic studies; oversaw regulatory documentation for an anti-CD25 humanized-antibody program.
Manager, Basic Research
2021–2023
Meridian Immune Therapeutics Inc., Seoul
Researcher
2019–2021
Xenotransplantation Research Center, HNU
Rhesus macaque tissue processing, longitudinal immune monitoring, CNS (brain/spinal cord) tissue handling.
Research Student, MOSAIC
2020–2023
Multi-Organ Single-cell Atlas of Immune Cells, Genomic Medicine Institute, HNU
Founding proposal; executed within the funded program (500+ donors across 6 organs): milestone tracking, multi-site QC, multi-PI coordination.
Selected Publications
01Reyes M*, Shelby T*, 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; ML classifier AUC 0.812; 702 samples, 251,055 CD4⁺ T cells.
02Shelby T*, 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." J. Neuroimmunology IF 2.9 · 2025. 11,587 cells, 10 populations.
03Shelby T*, Delgado J*, Moreau S, et al. "Deciphering Dysfunctional Regulatory T Cells in Vitiligo." Allergy IF 12.6 · 2025.
04Alvarez J*, Shelby T*, et al. "Long-term control of diabetes by baricitinib-based regimen after allo-islet transplantation in rhesus monkeys." Xenotransplantation IF 3.9 · 2024.
05Novak L*, Shelby T*, 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.
06Shelby T*, et al. "mTOR inhibitor-based immunosuppression in allogeneic islet transplantation." Islets IF 2.2 · 2019.
Co-author: eBioMedicine (IF 11.1, 2024) · JEADV (IF 9.2, 2024) · Current Diabetes Reports (IF 4.2, 2021). *Co-first = equal contribution.
Technical Skills
Single-cell / spatial / multi-omicscRNA-seq, scTCR-seq, snRNA/snATAC; Seurat, Scanpy, Squidpy, Monocle3, CellChat/NicheNet; scVI/scANVI, consensus NMF, embedding geometry; custom UMI-aware BAM-level isoform code (Python); Milo, GLIPH, InferCNV, weighted-LMM/EMM; GeoMx DSP; Olink proteomics.
Machine learning / DL / AIPython (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.
Experimental ground truth10x 5′/3′ scRNA + scTCR libraries; high-dim flow cytometry (24 markers), 6-way FACS; brain/CNS immune profiling; IHC/IF; two-photon; NHP CNS tissue (rhesus, cynomolgus, marmoset); EAE/MS and islet-transplant models.
Awards & Patents
Anti-CD25 Humanized Antibody, Patent 10202400918452024
Immunosuppression Composition, PI3K Inhibitor, Patent 10201434962172019
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, Microbiology & Immunology / IBRI, HNU. Computational co-corresponding.
jwbaek@hangang.ac.krDae-Ho Yoon, Ph.D.
Professor, Physiology, Nakdong University Wonju. Recent research supervisor.
dhyoon@nakdong.ac.kr