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Varun-U-Gowda/README.md

Hi, I'm Varun

Computational biologist focused on building reproducible omics workflows that turn sequencing data into interpretable biological and translational insights.

I work across single-cell RNA-seq, spatial transcriptomics, RNA+ATAC multiome, and bulk RNA-seq using Python, R, and reproducible workflow principles.

My GitHub highlights end-to-end projects in tumour microenvironment analysis, microglial regulatory genomics, spatial transcriptomics, and scalable genomics pipelines.

Technical Focus

  • Single-cell and single-nucleus RNA-seq analysis
  • Spatial transcriptomics and tissue microenvironment analysis
  • RNA+ATAC multiome and regulatory genomics
  • Bulk RNA-seq differential expression and pathway analysis
  • Reproducible pipeline development in Python, R, Git, and Nextflow

Background

Computational Biologist — Theomics International

Delivered end-to-end multi-omics analyses across 30+ client and research projects spanning RNA-seq, WGS, metagenomics, ChIP-seq, and miRNA-seq.

Bioinformatics Research Assistant — Brigham and Women's Hospital - Cox Lab

Analyzed microglial transcriptomics in Alzheimer's disease mouse models using bulk RNA-seq, DESeq2, quality control, pathway analysis, and biological interpretation.

M.S. Bioinformatics — Northeastern University

Connect

LinkedIn · Portfolio

Pinned Loading

  1. ad-microglia-multiome ad-microglia-multiome Public

    snRNA+snATAC multiome of AD DLPFC microglia — chromVAR motif analysis, WNN integration, peak-to-gene linkage, Monocle3 trajectory | Signac · Seurat · R

    R

  2. adar1-scrna-melanoma adar1-scrna-melanoma Public

    scRNA-seq of ADAR1-KO melanoma TME — pDC/monocyte ISG programs, PAGA pseudotime, TCGA SKCM survival validation | Scanpy · Python

    Python

  3. rna-seq-pipeline-deseq2 rna-seq-pipeline-deseq2 Public

    Modular DESeq2 downstream pipeline — tximport, outlier detection, VST, PCA, volcano plots | Applied to APP/PS1 microglial bulk RNA-seq (BWH) | R

    R

  4. Spatial_Transcriptomics_Visium Spatial_Transcriptomics_Visium Public

    10x Visium spatial transcriptomics pipeline — Squidpy, Moran's I, neighborhood enrichment, TLS-like niche detection | Workflow demonstration | Python

    Python

  5. Whole_Genome_Sequencing_Nextflow Whole_Genome_Sequencing_Nextflow Public

    Nextflow DSL2 WGS pipeline for microbial genomes — assembly, annotation, Kraken2 taxonomic profiling | Illumina · Nanopore · PacBio | Developed at BWH

    Nextflow