Joe Brown
Bioinformatics Engineer
Portland, Oregon, United States
Summary
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RockstarJoe Brown is a Bioinformatics Engineer with 13 years of experience building and modernizing production genomics workflows, currently driving bioinformatics engineering at Labcorp in Portland, Oregon. He has led migration to Nextflow and headed critical pipelines at Invitae, including bcl-to-fastq and germline reads-to-variants, while designing workflow reporting standards for CLIA/CAP compliance. His background spans academia, national labs, and industry—developing Snakemake-based metagenomics pipelines, instrument QC dashboards, and single-cell assembly workflows that improved turnaround and reduced compute costs. Joe has led cross-functional teams and managed project budgets as a principal investigator at PNNL, blending hands-on coding, pipeline validation, and operational leadership. He brings deep practical experience in reproducible workflow engineering and disaster recovery for clinical genomics, and a knack for turning complex sequencing operations into auditable, inspection-ready systems.
13 years of coding experience
12 years of employment as a software developer
Github Skills (116)
virus10
nmf10
snakemake10
package-management10
python10
cancer-genomics10
coverage10
genomics-visualization10
flask10
bam10
atlas10
data-analytics10
data-viz10
data-visualization10
bioconda10
Programming languages (15)
Github contributions (5)
brwnj/smoove-nf
Nov 2018 - Nov 2020
Nextflow implementation of the smoove workflow and other tools for SV calling and QC
Contributions:3 releases, 214 commits, 1 PR in 2 years
nextflow
pnnl/fqc
Mar 2018 - May 2019
:chart_with_upwards_trend: Extensible quality control dashboard built around FASTQ assessment.
Contributions:4 releases, 13 commits, 21 pushes in 1 year 2 months
fastqfastq-qadashboard
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