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.
Curriculum VitaeVol. XVIII · No. 1Boston Edition
Postdoctoral Applicant · Single-Cell & Spatial Multi-Omics
Barry Allen, Ph.D.
Computational biologist moving from single-cell and spatial multi-omics into connectome-scale neuroscience
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.
Scientific Interestssingle-cell & spatial multi-omics · cell-type inference from incomplete data · self-supervised / embedding representation learning · connectome × transcriptomics · computational neuroimmunology · reproducible ML/DL analysis
Education
M.S., Biomedical Sciences2012–2014
Hangang National University, Seoul
Thesis: Enhanced LPS-Induced Monocyte Activation by Recombinant Human Soluble CD180. Advisor: Min-Ho Suh, M.D., Ph.D.
B.S., Genetic Engineering2008–2012
Suwon Institute of Life Sciences, Suwon
Research & Experience
Postdoctoral Researcher2025–2026
Nakdong Univ. 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/MS multi-omic studies; oversaw regulatory documentation for an anti-CD25 humanized-antibody program.
Manager2021–2023
Meridian Immune Therapeutics Inc. · Basic Research, Seoul
Researcher2019–2021
Xenotransplantation Research Center, HNU · Seoul
Rhesus macaque tissue processing, longitudinal immune monitoring, CNS (brain/spinal cord) tissue handling.
Research Student · MOSAIC2020–2023
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.
Teaching Assistant2014–2016
HNU College of Medicine · Microbiology and Immunology
Selected Publications
01Reyes M*, Allen B*, 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.
02Allen B*, 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.
03Allen B*, Delgado J*, Moreau S, et al. "Deciphering Dysfunctional Regulatory T Cells in Vitiligo." Allergy IF 12.6 · 2025.
04Alvarez J*, Allen B*, et al. "Long-term control of diabetes by a baricitinib-based regimen after allo-islet transplantation in rhesus monkeys." Xenotransplantation IF 3.9 · 2024.
05Novak L*, Allen B*, et al. "Intra-tumoral heterogeneity and immune escape of melanoma from chronic UV photodamage by spatial gene expression." JEADV IF 9.2 · 2022.
06Allen B*, 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). *Co-first = equal contribution.
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; GeoMx DSP; Olink proteomics.
Machine learning / deep learning
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.
Experimental (domain ground truth)
10x 5′/3′ scRNA + scTCR libraries; high-dim flow cytometry (24 markers); brain/CNS immune profiling; IHC/IF; two-photon; NHP CNS tissue (rhesus, cynomolgus, marmoset); EAE/MS & islet-transplant models.
Awards & Patents
PatentAntagonistic Anti-CD25 Humanized Antibody2024
PatentImmunosuppression Composition w/ PI3K Inhibitor2019
AwardGrand Prize, AI Builders Hackathon (Nova)2024
AwardGrand Prize, Metro Innovation Workathon2023
AwardBest Poster, American Transplant Congress2017
Schol.NRF Ph.D. · 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