Jill V Hagey, MS, PhD

🐄 💩 🧬 💻 🐍 + 🇷 = 📊

Dr. Jill V. Hagey is a bioinformatics expert specializing in antimicrobial resistance (AMR), microbial genomics, and pipeline development for public health surveillance. With a PhD in Animal Biology and extensive experience in bioinformatics, I have successfully developed and deployed bioinformatic pipelines, including PHoeNIx, a widely used workflow for genomic surveillance of antibiotic-resistant pathogens.

Dr. Hagey serves as the Bioinformatics Domestic Lead for the CDC’s Antimicrobial Resistance Labortory Network, providing technical expertise, capacity-building support, and strategic guidance to public health jurisdictions. I has a proven track record of translating complex genomic data into actionable insights, collaborating across disciplines to modernize bioinformatic infrastructure, and mentoring scientists in bioinformatics and data science.

Expertise includes:
✔ Pipeline Development – Skilled in Nextflow, Snakemake, WDL, and cloud-based bioinformatics workflows (AWS, Terra.bio).
✔ Data Science & Machine Learning – Proficient in Python, R, and statistical modeling for microbial population analysis.
✔ Public Health & AMR Surveillance – Experienced in developing bioinformatics solutions for outbreak detection and genomic epidemiology.
✔ Technical Communication & Training – Recognized for effectively communicating complex concepts to diverse audiences, from lab personnel to leadership teams.

I am passionate about leveraging bioinformatics to enhance global public health surveillance, combat antimicrobial resistance, and modernize genomic data workflows.

Check out my tutorials page!

Email: jvhagey@gmail.com

GitHub  github LinkedIn  linkedin Research gate Google Scholar

Projects

  1. Rumen Sampling Methods Bias Bacterial Communities Observed github page and paper.
  2. Fecal Microbiome of Dairy Cattle github page and the paper.
  3. Projects studying passive immunity in dairy calves:
  4. Utility scripts I have written that I use for a varity of projects are found here.

Select Public Github Repositories I have Contributed To:

Cool Things:

Public Health and Bioinformatics Resources:

Helpful Workflows:

Stats Resources:

Machine Learning Resources:

Bioinformatic Resources: