J Holt
Staff Scientist, Bioinformatics
Huntsville-Decatur-Albertville Area United States
Summary
🤩
Rockstar🎓
Top SchoolJ Holt is a Staff Scientist in bioinformatics with 13 years of experience blending algorithms, clinical genomics, and software engineering to deliver production-ready sequencing analysis methods. With a PhD in computer science from UNC Chapel Hill and a track record at HudsonAlpha and PacBio, he focuses on long-read phasing, methylation, CNV calling, mitochondrial analysis and pharmacogenomics. He brings hands-on clinical pipeline development experience and a researcher's rigor—having supported the Undiagnosed Diseases Network and driven method validation in clinical labs. An active open-source maintainer in the bioconda ecosystem, he routinely packages and automates bioinformatics tools to improve reproducible deployments. Based in Huntsville, he combines systems-level engineering (from UAV collision testing to router firmware early in his career) with domain expertise in sequencing, making him adept at translating research algorithms into robust clinical and production tools.
13 years of coding experience
12 years of employment as a software developer
Master's, Computer Science, Master's, Computer Science at Auburn UniversityDoctor of Philosophy (Ph.D.), Computer Science, Doctor of Philosophy (Ph.D.), Computer Science at University of North Carolina at Chapel Hill
Github Skills (9)
bioinformatics10
conda10
bash10
package-management10
rust9
dockers5
docker5
github-ci4
githubaction-workflow4
Programming languages (12)
Github contributions (5)
bioconda/bioconda-recipes
Feb 2019 - Feb 2021
Conda recipes for the bioconda channel.
Role in this project:
DevOps Engineer & Package Maintainer
DevOps Engineer & Package MaintainerContributions:35 reviews, 2 commits, 42 PRs in 2 years
Contributions summary:J primarily contributes to the bioconda-recipes repository by adding and updating recipes for bioinformatics tools. The commits show the user working on build configurations, including modifications to build scripts (build.sh) and metadata files (meta.yaml), using bash and cargo for building tools. The contributions involve package management aspects such as version updates, sha256 checksum updates, and integrating external dependencies.
recipescondabiocondabioinformaticspackage-management
HudsonAlpha/CSL_public_benchmark
Dec 2021 - Jun 2022
Location of public benchmarking; primarily final results
Contributions:14 releases, 4 reviews, 49 commits in 6 months
benchmarklocationbenchmarking
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