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  • Johns Hopkins University

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jinyangye119/README.md

Yang Jin

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.

Featured Bioinformatics Projects

Project Focus
CellRelay Multicellular ligand-receptor relay motifs from single-cell and spatial data
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

Technical Strengths

  • 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

Contact

Pinned Loading

  1. CellRelay CellRelay Public

    R package for multicellular ligand-receptor relay motif analysis in single-cell and spatial transcriptomics

    R 3

  2. MetaLigand MetaLigand Public

    R package for non-peptide ligand activity and receptor-communication inference from transcriptomics

    R 3

  3. Mouse_CSC_PNAS Mouse_CSC_PNAS Public

    Reproducible figure-generation code for retinal degeneration snRNA-seq and snATAC-seq analysis

    R 1

  4. Prodecov Prodecov Public

    R package for prostate tumor purity prediction from proteomic abundance data

    R 2

  5. Retina-agent Retina-agent Public

    Retina-focused literature assistant workflow using PMC article retrieval and local LLM experiments

    R 1