Bioinformatician and computational biologist at Johns Hopkins working at the intersection of retinal degeneration, single-cell multiomics, lipid metabolism, and cell-cell communication.
I build reproducible analysis workflows and R tools for studying how aging, oxidative stress, metabolic dysregulation, and disease-associated cell states reshape tissue communication networks.
| Project | Focus |
|---|---|
| Single-cell-pipeline | Reproducible Nextflow workflow for single-cell RNA-seq analysis from count matrices through QC, integration, annotation, DEG, KEGG enrichment, and reporting |
| CellRelay | Multicellular ligand-receptor relay motifs from single-cell and spatial data |
| Retinal_Aging_Project | Comparative retinal aging analysis with R/Python workflows for single-cell, Xenium spatial, aging-clock, proximity, and cell-cell communication analyses |
| MetaLigand | Non-peptide ligand activity from transcriptomic data |
| Prodecov | Prostate tumor purity prediction from proteomics |
| Mouse_CSC_PNAS | Figure-generation code for retinal degeneration multiomics |
| HuiLab_ProstateCancer | Prostate cancer deconvolution workflows |
- R, Python, Bash, Linux, Git, and HPC workflows
- Single-cell and spatial transcriptomics: Seurat, Scanpy, Signac, ArchR, Xenium, MERFISH, and Visium
- Multi-omics integration, differential expression, enrichment analysis, trajectory analysis, and visualization
- Ligand-receptor analysis, communication networks, lipid metabolism, and non-peptide ligand inference
- Reproducible research packaging with documented inputs, scripts, examples, and public data links
- Google Scholar: https://scholar.google.no/citations?user=BteG8UIAAAAJ&hl=en
- GitHub: https://github.com/jinyangye119