Jesse Stombaugh
Senior Bioinformatics Scientist
Greater Fort Collins Area United States
Summary
👤
Senior🎓
Top SchoolJesse Stombaugh is a Senior Bioinformatics Scientist with 16 years of experience building Python-based pipelines for NGS data across amplicon, WGS/WES and RNA-Seq workflows. He designs scalable, production-ready solutions—containerized and deployed on AWS, Azure, and HPC—to handle large datasets and implement alignment, variant calling (SNPs/Indels, CNVs), and differential expression analyses. At Revvity and predecessors he led migration of pipelines into cloud-native systems, mentored teams, and contributed to peer-reviewed publications supporting gene modulation and editing products. An early contributor to the original QIIME project, he enhanced plotting and visualization features for microbial community analysis, a notable open-source footprint in bioinformatics. Trained to PhD level in biology with chemistry background, he combines deep domain science with practical software engineering to turn experimental needs into automated, auditable pipelines. Colleagues rely on him for pragmatic solutions that bridge wet-lab design (guides/primers) and rigorous computational QC.
17 years of coding experience
12 years of employment as a software developer
Doctor of Philosophy (PhD) Biology, Doctor of Philosophy (PhD) Biology at Bowling Green State UniversityBachelor of Science (BS) Chemistry, Bachelor of Science (BS) Chemistry at Hillsdale CollegeCertificate Bioinformatics and Proteomics/Genomics, Certificate Bioinformatics and Proteomics/Genomics at The University of Toledo
Github Skills (8)
data-visualizations10
data-visualization10
data-visualisation10
develop10
python10
matplotlib10
scientific-computing9
bioinformatics9
Programming languages (2)
Github contributions (5)
biocore/qiime
Sep 2009 - Aug 2012
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:484 commits in 3 years
Contributions summary:Jesse's contributions centered on improving the plotting functionality within the QIIME codebase, focusing on the generation of 2D and 3D PCoA plots. They made substantial changes to the visualization modules, incorporating the use of the 'colors' module and implementing new features, such as the ability to customize background colors and include various mapping file categories. The user also refactored code, fixed bugs and updated file output formats to enhance the user experience, ultimately providing for a more flexible user experience for generating heatmaps.
qiimemicrobiomeanalysis
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