14+ Years
Cross-disciplinary computational research and software delivery.
Bioinformatics | Biostatistics | Expedition Science
John L. Darcy, PhD
Senior Scientist (Bioinformatics) building reproducible, production-grade omics workflows and statistical tools for real-world research teams.
20+ R and Shiny Packages
Built production R and R Shiny packages, including several commercialized tools.
44+ Publications
Peer-reviewed contributions across microbiome and omics research.
What I Build
Technical depth with production outcomes
Pipeline Engineering
Designed and scaled cloud-native ONT metabarcoding workflows with 65+ amplicons on AWS, from prototype through production delivery.
Performance + Reliability
Reduced QA and QC processing turnaround by 98 percent through automation and reproducible architecture.
Applied Statistical Methods
Improved GSEA performance by about 1.5x while increasing statistical power by up to 20 percent.
Tooling for Scientists
Built multiple production R packages and Shiny tools that make high-dimensional data usable by non-computational stakeholders.
Trajectory
Research, software, and team leadership
Senior Scientist (Bioinformatics) - Jonah Ventures
Leads production bioinformatics engineering for eDNA and metagenomics workflows, including cloud analytics and customer-facing outputs.
Bioinformatics Scientist - Standard BioTools (formerly SomaLogic)
Delivered production analytical software, accelerated assay quality control workflows, and supported cross-functional translational analyses.
NIH NLM Computational Biology Fellow - CU Anschutz
Published statistical methods and software for microbiome data, including the R + C++ package specificity.
Postdoctoral Researcher (Mycology) - University of Hawaii
Built sequencing pipelines for multi-terabyte ITS datasets and led team projects in ecological genomics.
Academic Background
Education and Postdoctoral Training
NIH NLM Computational Biology Postdoctoral Fellowship
University of Colorado Anschutz Medical Campus
Developed and published statistical methods and software for microbiome analysis, including the R and C++ package specificity.
Postdoctoral Researcher (Mycology)
University of Hawaii at Manoa
Built multi-terabyte sequencing pipelines and applied spatial and machine learning approaches to ecological genomics.
PhD, Ecology and Evolutionary Biology
University of Colorado Boulder
Completed doctoral research in microbial ecology, biogeography, and model-driven analysis of extreme and glacial ecosystems.
Certificate, Protected Health Information (PHI) Use
University of Colorado Anschutz Medical Campus
Formal training in compliant handling of sensitive clinical data for analysis workflows and research operations.
BA, Molecular, Cellular, and Developmental Biology
University of Colorado Boulder
Built foundational training in molecular biology and experimental science that informs downstream computational work.
Expedition Work
Science in places most people only see in documentaries
Antarctica - McMurdo Dry Valleys
Atacama Andes - Volcan Llullaillaco
Peruvian Andes - Puca Glacier
Alaska - Denali National Park
Hawaii - Native montane ecosystems
Publication Record
Publications and Research Output
Contact and Documents