Computational Biology

What I do

I design scalable, reproducible computational frameworks for microbiome multi-omics—optimized for high-performance computing (HPC) systems and large-scale ecological datasets.

Core Areas

Workflow Automation and Pipelines
Snakemake • SLURM • Shell scripting
  • Snakemake-driven workflow architecture
  • SLURM job scheduling and resource-aware pipeline design
  • Fully automated multi-step bioinformatics pipelines
  • Reproducible multi-omics workflows across large datasets
  • HPC optimization (CPU/memory tuning, job arrays, logging strategies)
HPC, Cloud & Environment Management
SLURM • Palmetto Cluster • Conda • Modules
  • SLURM-based HPC workflow management
  • Experience with Palmetto Cluster and shared computing environments
  • Conda / mamba environment creation and dependency isolation
  • HPC module systems and software stack troubleshooting
  • Resource scaling for genome-resolved and multi-omics projects
Machine Learning & Statistical Computing
scikit-learn • Linear models • Multivariate ecology
  • scikit-learn for applied classification and regression workflows
  • Linear and mixed-effects models (when appropriate)
  • Multivariate ecological statistics in R (vegan and related tools)
  • Bray–Curtis dissimilarity, PERMANOVA, RDA, db-RDA
  • PCA / PCoA, clustering, ordination, ecological modeling
Version Control & Reproducibility
Git • GitHub • Structured project design
  • Git-based version control for research workflows
  • GitHub repositories for transparent and collaborative development
  • Branch-based workflow management
  • Structured README documentation and reproducible project organization
Visualization & Scientific Figure Design
R • Python • Illustrator • Inkscape
  • ggplot2 for publication-grade statistical graphics
  • Python matplotlib (and seaborn when appropriate)
  • High-quality scientific figure production
  • Final figure polishing and layout design (Adobe Illustrator, Inkscape)
Operating Systems
Linux • macOS • Windows
  • Linux-based research environments (primary development platform)
  • macOS and Windows workflow compatibility
  • Cross-platform troubleshooting and reproducible environment setup