Spencer Mahaffey
Principal Information Technology Professional
Aurora, Colorado, United States
Summary
👤
Senior🎓
Top SchoolSpencer Mahaffey is a Principal Information Technology Professional and bioinformatics software engineer with over two decades of scientific software development experience and 13 years in applied roles bridging biology and engineering. He designs and maintains scalable genomics platforms (notably phenogen.org), migrating legacy databases to AWS Aurora and building responsive single-page genome/transcriptome browsers with D3.js that summarize array, RNA-Seq, and strain-specific sequence data. Spencer combines hands-on lab experience in omics, proteomics, and metabolomics with strong backend skills—optimizing RNA-Seq pipelines for HPC, inventing novel smallRNA quantification methods, and reworking data storage to enable parallel processing and lower memory footprints. He manages full-stack site operations, performance tuning, and user-facing visualizations, prioritizing throughput and cost-efficiency for research-driven services. Based in Aurora, Colorado, he holds a Master of Engineering in Computer Science and leverages his molecular biology background to translate complex experimental needs into maintainable, high-performance software.
13 years of coding experience
Bachelor of Science, Computer Science, Bachelor of Science, Computer Science at University of WyomingMaster of Engineering, Computer Science, Master of Engineering, Computer Science at University of Colorado Boulder
English
Github Skills (19)
genetics8
bioinformatics7
prediction6
rna-seq6
seq6
sequencing5
transcript5
assembly4
gene-expression4
genomics4
pipeline3
bioconda3
thermostat1
iot-application1
google-home1
Programming languages (6)
Github contributions (5)
TabakoffLab/PhenoGenRESTR
Jun 2022 - May 2024
Contributions:2 releases, 24 pushes, 1 branch in 1 year 10 months
TabakoffLab/PhenogenCloud
Apr 2018 - Mar 2025
New version of Phenogen built to run in the cloud.
Contributions:3 PRs, 221 pushes, 6 branches in 7 years
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