BA
Curriculum Vitae
Barry Allen
Computational single-cell scientist. Single-cell and spatial multi-omics toward connectome-scale neuroscience.
Boston, MA
(555) 019-2847
barry.allen@example.com
Google Scholar
(555) 019-2847
barry.allen@example.com
Google Scholar
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. My objective: connect molecular cell identity to circuit structure and function by integrating connectomics with transcriptomics, growing into connectome-constrained circuit models.
Publication Record
Interests. Cell-type inference from incomplete data; self-supervised representation learning; connectome × transcriptomics; computational neuroimmunology.
Education
Ph.D., Biomedical Sciences
2014–2023
Hangang National University · Seoul
Dendritic Cell Heterogeneity Across Chronic Inflammatory Contexts. Advisor: Min-Ho Suh.
M.S., Biomedical Sciences
2012–2014
Hangang National University · Seoul
LPS-Induced Monocyte Activation by Soluble CD180.
B.S., Genetic Engineering
2008–2012
Suwon Institute of Life Sciences · Suwon
Experience
Postdoctoral Researcher
2025–2026
Nakdong Univ. Wonju College of Medicine · Physiology / Organelle Medicine RC
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 anti-CD25 antibody regulatory documentation.
Researcher
2019–2021
Xenotransplantation Research Center, HNU · Seoul
Rhesus macaque tissue processing, longitudinal immune monitoring, CNS tissue handling.
Research Student, MOSAIC
2020–2023
Multi-Organ Single-cell Atlas of Immune Cells, HNU · Genomic Medicine Institute
Founding proposal; executed within the funded program (500+ donors, 6 organs): milestone tracking, multi-site QC, multi-PI coordination.
Selected Publications · First / co-first author
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.
Technical Skills
Single-cell / spatial / multi-omic. scRNA-seq, scTCR-seq, snRNA/snATAC; Seurat, Scanpy, Squidpy, Monocle3, CellChat/NicheNet; scVI/scANVI, consensus NMF; custom UMI-aware BAM-level isoform code (Python); Milo, GLIPH, InferCNV; GeoMx DSP; Olink proteomics.
Machine learning / DL / AI. Python (scikit-learn, XGBoost/LightGBM/CatBoost, PyTorch); AUC-validated classifiers; VAE/GAN/GNN; multimodal DL (imaging + transcriptomic + clinical); AlphaFold2/3, ProteinMPNN, DiffDock; Linux, R, Git.
Experimental. 10x 5′/3′ scRNA + scTCR libraries; high-dim flow cytometry (24 markers); brain/CNS immune profiling; IHC/IF; two-photon; NHP CNS tissue; EAE/MS and islet-transplant models.
Awards & Patents
Anti-CD25 Humanized Antibody (Patent)2024
PI3K Inhibitor Composition (Patent)2019
Grand Prize, AI Builders Hackathon2024
Grand Prize, Metro Innovation Workathon2023
Best Poster, ATC Chicago2017
NRF · BK21 Plus · HNU Dean's2014–20
Reference
Min-Ho Suh, M.D., Ph.D.
HNU College of Medicine; CEO/CSO, Meridian Immune. Ph.D. advisor.
mhsuh@hangang.ac.kr
mhsuh@hangang.ac.kr
Reference
Ji-Won Baek, M.D., Ph.D.
HNU, Microbiology & Immunology / IBRI. Computational co-corresponding.
jwbaek@hangang.ac.kr
jwbaek@hangang.ac.kr
Reference
Dae-Ho Yoon, Ph.D.
Nakdong Wonju, Physiology. Recent research supervisor.
dhyoon@nakdong.ac.kr
dhyoon@nakdong.ac.kr