Sr. Bioinformatics Engineer (DGI Start Up)

Position Summary

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.

Essential Functions

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.

Focus Areas

Genome Assembly

You will lead the innovation and deployment of next-generation assembly pipelines built for long-read sequencing technologies (PacBio HiFi, ONT, and hybrid approaches). Your objective: produce high-quality, telomere-to-telomere (T2T) assemblies that resolve complex genomic architecture with near-perfect continuity. 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.

Genome Annotation

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. This includes mapping methylation states, characterizing microRNAs and other non-coding RNA families, annotating regulatory chromatin packaging, and identifying transposable elements that influence genome structure and disease.

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. By synthesizing these diverse signals into coherent, high-resolution annotations, you will help build a genomic interpretation engine capable of powering next-generation diagnostics and predictive models.

Human Pangenomics

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.

Transformer & Generative AI for Genomics

You will design and implement advanced transformer-based and generative AI architectures that learn from large-scale genomic and multi-omic datasets. Applications may include sequence-to-function modeling, variant-effect prediction, structural variant interpretation, sequence generation, imputation, and multimodal fusion. These models will serve as intelligent engines that power early disease prediction, mechanistic understanding, and therapeutic discovery.

Prerequisites

• 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

Work Environment
The work environment characteristics described here are representative of those a teammate encounters while performing the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

• Moderate noise (i.e. business office with computers, phone, and printers, light traffic)
• Ability to work in a confined area.
• Ability to sit at a computer terminal for an extended period of time.

Physical Demands
The physical demands described here are representative of those that must be met to successfully perform the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

• While performing the duties of this job, the employee is regularly required to, stand, sit; talk, hear, and use hands and fingers to operate a computer and telephone keyboard reach, stoop kneel to install computer equipment
• Specific vision abilities required by this job include close vision requirements due to computer work
• Light to moderate lifting is required

J. Craig Venter Institute is an Equal Opportunity Employer. All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other legally protected characteristic or status.