J. Craig Venter Institute · 19 hours ago
Sr. Bioinformatics Engineer (DGI Start Up)
San Diego, CA
Full-time
Onsite
Senior Level, Lead/Staff
$116K/yr - $180K/yr
10+ years expJ. Craig Venter Institute is a state-of-the-art human genomics startup focused on improving disease prediction, diagnosis, and treatment. The Senior Bioinformatics Engineer will architect computational systems for precision genomics, collaborating with scientists to build advanced pipelines and AI models that analyze large genomic datasets.
BiotechnologyGeneticsHealth CareNon Profit
Responsibilities
You will architect foundational computational systems that drive our precision genomics platform
You will lead the innovation and deployment of next-generation assembly pipelines built for long-read sequencing technologies (PacBio HiFi, ONT, and hybrid approaches)
You will develop methods to handle repetitive regions, structural variants, segmental duplications, centromeric regions, and other difficult-to-assemble sequences—pushing completeness and accuracy to new scientific frontiers
You will architect advanced annotation pipelines capable of reconstructing the functional and regulatory landscape of the genome with single-base precision
Your work will integrate transcriptomic, epigenomic, and long-read sequencing datasets to reveal multi-layered biological meaning
You will develop tools that reliably label exons, introns, splice junctions, gene promoters, enhancers, catalytic elements, and other functional domains critical for understanding early-stage disease biology
You will help build a genomic interpretation engine capable of powering next-generation diagnostics and predictive models
You will be a key contributor to scaling our human pangenome initiative by developing graph-based models and population-scale comparative methods that capture the full spectrum of human genetic diversity
Your algorithms will enable more accurate variant representation, improved structural variant detection, and equitable genomic insights across diverse ancestry groups—building a pangenomic foundational database that supports global precision medicine
You will design and implement advanced transformer-based and generative AI architectures that learn from large-scale genomic and multi-omic datasets
Qualification
Required
Master's degree with 10+ years of experience, or PhD with post-graduate specialization in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related field
Deep expertise in genome assembly (including long-read and T2T assembly pipelines)
Experience with genome annotation, regulatory genomics, or multi-omic integration
Proven ability to design and implement production-grade bioinformatics software and scalable computational systems
Strong programming skills (Python, C/C++, Rust, Go, or similar) and proficiency with cloud/HPC computing
Experience developing or applying transformer or generative AI models in scientific or technical contexts
A track record of innovation demonstrated by impactful tools, publications, patents, or products
A passion for working in a fast-paced, ambitious startup environment where creativity, ownership, and impact matter
Company
J. Craig Venter Institute
J. Craig Venter Institute is a non-profit organization engaged in the research of genomics.
51-200 employees
H1B Sponsorship
J. Craig Venter Institute has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (5)
2024 (2)
2023 (2)
2022 (3)
2021 (6)
2020 (2)
Funding
Current Stage
Growth StageTotal Funding
$32.7MKey Investors
The Conrad Prebys FoundationNational Institutes of Health
2024-10-02Grant· $5M
2024-09-18Grant· $0.3M
2014-06-05Grant· $25M
Leadership Team
Heather Kowalski
COO
Jill Mullen
SVP, Philanthropy & Alliances
Recent News
2025-10-01
2025-08-08
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