Matthew Sooknah
Staff Machine Learning Engineer at Calico Life Sciences
San Francisco, California, United States
Summary
🤩
Rockstar🎓
Top SchoolMatthew Sooknah is a Staff Machine Learning Engineer with 13 years of experience building ML-driven systems at the intersection of biology and computational science, currently based in San Francisco. He progressed through platform and senior ML roles at Calico after formative engineering and scientist positions at 10x Genomics and the Broad Institute, blending production software skills with domain expertise in genomics. His open-source contributions to flagship tools like GATK and Picard show deep backend work on critical sequencing formats and utilities—porting core modules, improving SAM/FASTQ processing, and tightening unit tests. Comfortable moving between research and production, he has a physics BS from MIT and a track record of shipping robust, data-intensive pipelines. Colleagues rely on him for pragmatic solutions that bridge algorithmic rigor and operational reliability. A less obvious strength is his sustained focus on maintainability and migration work that preserves legacy genomics functionality while enabling modern ML workflows.
13 years of coding experience
11 years of employment as a software developer
Bachelor of Science (BS) Physics, Bachelor of Science (BS) Physics at Massachusetts Institute of Technology
Github Skills (10)
bioinformatics10
javas10
gatk10
java10
testing10
bam9
vcf-files9
sam9
cra9
unit-testing8
Programming languages (7)
Github contributions (5)
broadinstitute/gatk
Jan 2015 - Apr 2015
Official code repository for GATK versions 4 and up
Role in this project:
Back-end Developer
Back-end DeveloperContributions:13 commits, 5 comments in 2 months
Contributions summary:Matthew's commits primarily involve porting and migrating code related to the `picard.sam` module within the GATK repository. These changes include moving existing code files, and implementing core functionalities like converting Fastq files to SAM files, estimating library complexity, and comparing SAM files. The contributions are essential for maintaining and updating the GATK's core functionalities related to sequence alignment and processing. The user also made several bug fixes and unit test improvements within the `SamComparison` class.
genomesciencednaspark-mlngs
broadinstitute/picard
Oct 2014 - Dec 2015
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Role in this project:Back-end Developer
Back-end DeveloperContributions:27 commits, 18 PRs, 65 pushes in 1 year 1 month
Contributions summary:Matthew primarily contributed to the `picard` repository, a Java-based tool for manipulating high-throughput sequencing data. Their commits demonstrate a focus on refining existing functionalities, including modifying Java code related to genotype concordance and sequencing artifact analysis. The user also fixed compile errors and addressed aesthetic issues within the documentation generation process. These changes indicate a role in maintaining and improving core functionalities within the project.
sequencebamcramcommand-line-toolsfasta
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