Jonathan Smith
Associate Director Of Computational Methods
Boston, Massachusetts, United States
Summary
🤩
Rockstar🎓
Top SchoolJonathan Smith is an associate director and computational methods leader with nine years of professional experience and a decade-plus background in scientific software engineering across industry and research institutions. Based at the Broad Institute after senior engineering roles there and at BAE Systems, he blends deep back-end engineering with domain expertise in genomics—contributing notable enhancements to flagship open-source tools like GATK and Picard to improve variant annotation, file handling, and locus iteration. Trained in neuroscience and computer science, he excels at translating messy biological data into robust, production-grade pipelines and tools. Colleagues describe him as a pragmatic innovator who moves fluidly between hands-on coding and strategic platform design, and he even paused for a sabbatical that included time in Tokyo and Kyoto, reflecting an appetite for broadening perspective.
8 years of coding experience
16 years of employment as a software developer
High School Diploma, High School Diploma at Boston Latin SchoolCandidate for Bachelor of Science Computer Science, Candidate for Bachelor of Science Computer Science at Northeastern UniversityBachelor of Science (BS) with Honors Neuroscience and Computer Science, Bachelor of Science (BS) with Honors Neuroscience and Computer Science at Brandeis University
Github Skills (12)
bioinformatics10
javas10
command-line-tool10
algorithms10
data-structures10
cra10
bam10
data-structure10
java10
vcf-files10
sam10
algorithm8
Programming languages (17)
Github contributions (5)
broadinstitute/gatk
Jun 2017 - Jul 2022
Official code repository for GATK versions 4 and up
Role in this project:
Back-end Developer & Bioinformatics Specialist
Back-end Developer & Bioinformatics SpecialistContributions:151 reviews, 439 commits, 232 PRs in 5 years 2 months
Contributions summary:Jonathan contributed significantly to the GATK (Genome Analysis Toolkit) project, primarily focusing on improving and extending the functional annotation capabilities. Their commits added checks for and addressed issues with sequence dictionaries and file handling. The user also added a range of functionalities, from processing and improving ENSEMBL GTF files to adding in support for symbolic alleles and implementing custom variant classification orders. These changes enhanced the usability and accuracy of the software.
genomesciencednaspark-mlngs
broadinstitute/picard
Jun 2019 - Sep 2019
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:13 commits, 3 PRs, 10 pushes in 3 months
Contributions summary:Jonathan primarily contributed to the `CollectSamErrorMetrics` tool within the Picard repository, focusing on modifying and enhancing its functionality. Their work involved addressing code review comments, splitting iteration functionalities and updating the VCF data source, and improving the process of iterating over loci. The user made changes to improve how the tool processes input data from BAM, VCF, and reference files.
sequencebamcramcommand-line-toolsfasta
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