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!
GitHub LinkedIn Research gate Google Scholar
Projects
- Rumen Sampling Methods Bias Bacterial Communities Observed github page and paper.
- Fecal Microbiome of Dairy Cattle github page and the paper.
- Projects studying passive immunity in dairy calves:
- Determining how serum IgG is related to mortality in the first 4 months of life in dairy heifers
- Clinincal trial of plasma as a treatment for failure of passive transfer in dairy calves
- Evaluating the half-life of IgG from colstrum, colostrum replacer or bovine plasma
- Assesment of a commercial refractometer for onside evaluation of serum IgG and total milk solids
- Evalution of failure of passive transfer rates in calves either bottle or tube fed colostrum
- Utility scripts I have written that I use for a varity of projects are found here.
Select Public Github Repositories I have Contributed To:
- 🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
- nf-core modules
- Containers for the Waterborne Diseases Prevention Branch at CDC.
- Technical Outreach and Assistance for States Team (TOAST) developed benchmark datasets for SARS-CoV-2 sequencing.
Cool Things:
- Bioinformatics Chat podcast
- Bioinformatics Virtual Coordination Network
- Micro Binfie (Microbial Bioinformatics) Podcast
Public Health and Bioinformatics Resources:
- Public Health Bioinformatics
- Public Health Alliance for Genomic Epidemiology (PHA4GE)
- StaPH-B (State Public Health Bioinformatics Workgroup and their Github
Helpful Workflows:
- 16S rRNA gene amplicon workflow from Holmes Lab
- Statistical Methods in Microbiome Research Workshop
- Happy Belly Bioinformatics
- Statistical Diversity Lab blog: Microbiome data analysis 101
Stats Resources:
- Modern Statistics for Modern Biology
- Statistical Rethinking: A Bayesian Course Using R and Stan
- Biomedical Data Science Text
Machine Learning Resources:
- Resource Lists
- Examples and page with code.