Curriculum Vitae · Established Record in Single-Cell Science
ALFRED PENNYWORTH, Ph.D.
Computational biologist moving from single-cell & spatial multi-omics into connectome-scale neuroscience
Boston, MA 02135 T (555) 019-2847 E alfred.pennyworth@example.com Google Scholar alfredpennyworth.example.com/cv

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.

Interests: single-cell & spatial multi-omics; cell-type inference from incomplete data; self-supervised representation learning; connectome × transcriptomics; computational neuroimmunology.

Publication Record

18Total
17Peer-reviewed
6First / co-first
1Under review
1Reyes M*, Pennyworth A*, 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.
2Pennyworth A*, 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.
3Pennyworth A*, Delgado J*, Moreau S, et al. "Deciphering Dysfunctional Regulatory T Cells in Vitiligo." Allergy IF 12.6 · 2025.
4Alvarez J*, Pennyworth A*, et al. "Long-term control of diabetes by a baricitinib-based regimen after allo-islet transplantation in rhesus monkeys." Xenotransplantation IF 3.9 · 2024.
5Novak L*, Pennyworth A*, 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.
6Pennyworth A*, et al. "mTOR inhibitor-based immunosuppression in allogeneic islet transplantation." Islets IF 2.2 · 2019.
Selected co-author: eBioMedicine (IF 11.1, 2024), JEADV (IF 9.2, 2024), Current Diabetes Reports (IF 4.2, 2021). * denotes equal contribution.

Experience

Postdoctoral Researcher2025–2026
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 Director2023–2025
Meridian Immune Therapeutics Inc. · Basic Research, Seoul
Built in-house single-cell & spatial transcriptomics code from scratch; led cross-functional NHP (cynomolgus, marmoset) EAE/MS multi-omic studies; oversaw regulatory documentation for an anti-CD25 humanized-antibody program.
Manager, Basic Research2021–2023
Meridian Immune Therapeutics Inc. · 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
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.

Education

Ph.D., Biomedical Sciences2014–2023
Hangang National University · Seoul
Mapping Dendritic Cell Heterogeneity Across Chronic Inflammatory Contexts. Advisor: Min-Ho Suh, M.D., Ph.D.
M.S., Biomedical Sciences2012–2014
Hangang National University · Seoul
Enhanced LPS-Induced Monocyte Activation by Recombinant Human Soluble CD180.
B.S., Genetic Engineering2008–2012
Suwon Institute of Life Sciences · Suwon

Technical Skills

Single-cell / spatial / multi-omicscRNA-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, 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); vision-language transformers; AlphaFold2/3, ProteinMPNN, DiffDock, MolFormer; Linux, R/RStudio, Git.
Experimental (domain ground truth)10x 5′/3′ scRNA + scTCR libraries; high-dimensional flow cytometry (24 markers), 10-color FACS; brain/CNS immune profiling; IHC/IF (frozen & FFPE); two-photon microscopy; NHP CNS tissue (rhesus, cynomolgus, marmoset); EAE/MS & islet-transplant models.

Awards & Patents

Antagonistic Anti-CD25 Humanized Antibody (Patent 1020240091845)2024
Immunosuppression Composition w/ PI3K Inhibitor (Patent 1020143496217)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's Support2014–2020

Selected Presentations

Poster: KAI Annual Meeting, Incheon (2022); Cytokine, Hawaii (2022); American Transplant Congress, Chicago (2017); The Transplantation Society, Hong Kong (2016); IPITA/IXA/CTS, Melbourne (2015); TREG, Shanghai (2012).

References

Min-Ho Suh, M.D., Ph.D.
Professor, HNU College of Medicine; CEO/CSO, Meridian Immune Therapeutics. Ph.D. advisor.
mhsuh@hangang.ac.kr
Ji-Won Baek, M.D., Ph.D.
Assistant Professor, Microbiology & Immunology / IBRI, HNU. Computational co-corresponding.
jwbaek@hangang.ac.kr
Dae-Ho Yoon, Ph.D.
Professor, Physiology & Global Medical Science, Nakdong Wonju. Recent supervisor.
dhyoon@nakdong.ac.kr
Korean (native) · English (professional working) · References available on request