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  • Amsterdam University Medical Centers
  • Amsterdam

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utkarsh0493/README.md

๐Ÿ‘‹ Hi, I'm Utkarsh Mahamune

I'm a Marie Skล‚odowskaโ€‘Curie COFUND PhD researcher at Amsterdam University Medical Centers (AMC), blending computational biology, bioinformatics, and systems modeling to tackle complex biomedical problems in autoimmune disorders like rheumatoid arthritis.

๐Ÿงฌ What I Work On

  • Single-cell & spatial transcriptomics (10x Visium, Xenium, Seurat, Scanpy)
  • Deconvolution benchmarking (RCTD, CARD, SPOTlight, etc.)
  • Modeling cell behavior using ODEs, SSA, and parameter estimation tools
  • Building reproducible pipelines with R, Python, and workflow managers
  • Translating data insights for clinicians, lab scientists, and healthcare teams

๐Ÿš€ Featured Work

  • ENCORE โ€“ A reproducibility framework adopted in 70+ projects
    ๐Ÿ“„ Nature Communications, 2024
    Focus: Reproducible science, digitalization, and collaborative tools

  • Systematic evaluation of robustness to cell type mismatch of deconvolution methods for spatial transcriptomics data
    ๐Ÿ“„ bioRxiv, 2025
    Focus: Deconvolution methods, Robustness

  • Xenium ST Pipelines โ€“ Custom ROI-based workflows for spatial data
    Working with 13+ samples across multiple tissues and experimental designs

๐Ÿ›  Tech Stack

R | Python | Seurat | Scanpy | Giotto | Nextflow | Docker
GitHub | renv | GillespieSSA2 | Shiny | SpatialExperiment | Apptainer

๐ŸŒฑ Currently Learning

  • Generative AI with HuggingFace & JAX
  • Advanced ML for spatial genomics
  • Modular pipeline design for high-throughput multi-omics

๐Ÿ’ฌ Let's Connect!

Pinned Loading

  1. FSS-Nav-App FSS-Nav-App Public

    Privacy-first local Streamlit app for navigating computational research projects.

    Python

  2. ENCORE ENCORE Public

    Forked from EDS-Bioinformatics-Laboratory/ENCORE

    ENCORE: Enhancing Computational Reproducibility

    Python 1

  3. ENCORE_AUTOMATION ENCORE_AUTOMATION Public

    Forked from EDS-Bioinformatics-Laboratory/ENCORE_AUTOMATION

    ENCORE_AUTOMATION

    HTML

  4. FSS-Navigator FSS-Navigator Public

    Forked from EDS-Bioinformatics-Laboratory/FSS-Navigator

    Utkarsh Mahamune, Antoine van Kampen, Aldo Jongejan: The standardized file system structure (FSS) navigator

    HTML 1

  5. Robustness_evaluation_deconv_methods Robustness_evaluation_deconv_methods Public

    Forked from EDS-Bioinformatics-Laboratory/Robustness_evaluation_deconv_methods

    Author: Utkarsh Mahamune | Systematic evaluation of robustness to cell type mismatch of deconvolution methods for spatial transcriptomics

    R 1

  6. scRNAseq-analysis-notes scRNAseq-analysis-notes Public

    Forked from Zhuang-Bio/scRNAseq-analysis-notes

    scRNAseq analysis notes from Ming Tang