Ted Brookings
Staff Computational Biologist
Malden, Massachusetts, United States
Summary
🤩
Rockstar🎓
Top SchoolTed Brookings is a Staff Computational Biologist with nine years of industry experience building production-grade bioinformatics and analysis pipelines, currently at Fulcrum Genomics in Malden, MA. He spent five years on the Broad Institute’s Structural Variants team contributing to GATK, where his DevOps and backend work helped automate cloud-native SV discovery workflows and improve core Java tools for breakpoint evidence and annotation. Earlier roles span image-analysis leadership at Q-State—developing segmentation, signal processing, and cloud pipelines for fluorescent electrophysiology—and computational neuroscience research modeling single-neuron dynamics. He combines deep quantitative training (PhD in Physics, MS in Mathematics) with hands-on scripting and Spark/Dataproc automation to move methods from algorithm to scalable production. Notably, his open-source contributions to the widely used broadinstitute/gatk repo reflect a rare blend of algorithmic insight and practical engineering that reduces friction in large-scale genome analysis.
9 years of coding experience
10 years of employment as a software developer
Virginia TechDoctor of Philosophy (PhD), Physics, Doctor of Philosophy (PhD), Physics at University of California, Santa Barbara
Github Skills (18)
google-cloud-platform10
spark10
bash10
gcp10
script10
google-cloud10
bioinformatics10
git9
java9
dataproc9
javas9
genome8
genomics8
genomes8
cicd7
Programming languages (7)
Github contributions (5)
broadinstitute/gatk
Jul 2017 - Jan 2023
Official code repository for GATK versions 4 and up
Role in this project:
DevOps Engineer & Backend Developer
DevOps Engineer & Backend DeveloperContributions:2 reviews, 22 commits, 21 PRs in 5 years 7 months
Contributions summary:Ted primarily contributes to the management and improvement of the GATK pipeline, focusing on automating the SV (Structural Variation) discovery workflow within a cloud environment. Their commits involve creating and modifying scripts (Bash) to create and manage Dataproc clusters, run Spark jobs, copy results to cloud storage, and automate the overall pipeline execution. The user also makes code changes that directly impact the underlying Java codebase, implementing enhancements and fixing bugs related to breakpoint evidence and annotations.
genomesciencednaspark-mlngs
TedBrookings/dockers
Mar 2019 - Sep 2022
Contributions:19 pushes, 4 branches in 3 years 6 months
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