Sr. Bioinformatics Engineer (DGI Start Up)

J. Craig Venter Institute • San Diego, CA

14d

About The Position

Are you a visionary developer or computational scientist ready to help build the future of human health? Do you thrive in fast-moving, mission-driven environments where your ideas shape breakthrough technologies? If so, we want you to join our state-of-the-art human genomics startup company created to radically improve how we predict, diagnose, and treat early-stage diseases. We are assembling an elite team of senior-level innovators in bioinformatics, human pangenomics, and AI-driven genomics to power our next wave of scientific and technological advancement. You will work on technology with the potential to transform global health outcomes while collaborating with leaders in genomics, AI, and precision medicine. You will help to shape the foundational software and science of a next-generation biotech company with a mission-driven culture that values bold thinking, scientific rigor, and meaningful impact. Competitive salary commensurate with experience and qualifications. As a Senior Bioinformatics Engineer, you will architect foundational computational systems that drive our precision genomics platform. You ll work with world-class scientists and engineers to build advanced pipelines, algorithms, and AI models that unlock new insights from massive genomic datasets. This is a high-impact, high-ownership role in a rapidly growing organization where you will need to have significant experience in at least one of the below four focus areas.

Requirements

• 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

Responsibilities

• Lead the innovation and deployment of next-generation assembly pipelines built for long-read sequencing technologies (PacBio HiFi, ONT, and hybrid approaches).
• 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.
• Architect advanced annotation pipelines capable of reconstructing the functional and regulatory landscape of the genome with single-base precision.
• 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.
• Develop graph-based models and population-scale comparative methods that capture the full spectrum of human genetic diversity.
• Design and implement advanced transformer-based and generative AI architectures that learn from large-scale genomic and multi-omic datasets.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Number of Employees: 101-250 employees