Full Stack Software Engineer Jobs in Waltham, MA

This role strongly prefers candidates located in the Boston area with the ability to regularly commute to our Seaport headquarters.

Due to the nature of this role, candidates should expect to support U.S. Government customers. Candidates must have the ability to obtain and maintain a U.S. security clearance per business requirements. In connection therewith, candidates must be willing to undergo a background investigation and meet eligibility requirements. Clearance sponsorship will be available.
Candidates who currently hold an active or recently inactive U.S. Government security clearance are encouraged to apply.

Ginkgo Biosecurity is building next-generation biosecurity infrastructure to help governments and partners detect, attribute, and deter biological threats. Our mission extends across public health, national security, and global defense, ensuring nations can rapidly identify dangerous pathogens, understand where threats originate, and respond with confidence.

We are seeking a Senior Full-Stack Software Engineer to join the Biosecurity engineering team. This role is ideal for someone who thrives in cross-disciplinary environments and is excited to build production software that directly supports biosecurity, epidemiology, and biological data workflows. We are looking for an engineer who is not only a technical expert but also a forward-thinker who embraces AI-augmented development and maintains a 'deploy-with-confidence' culture through rigorous CI/CD and automated testing

You will work across the stack-from backend services and data pipelines to user-facing web applications-building reliable, scalable systems that turn complex biological data into actionable insights.

Responsibilities

• Develop high-performance full-stack applications that translate complex biological data and operational needs into intuitive software using Python and modern JavaScript frameworks
• Champion an AI-first mindset, leveraging generative AI tools and LLM-based assistants to accelerate feature development, optimize code quality, and automate routine engineering tasks
• Collaborate with cross-functional domain experts to architect and operate on biological datasets (genomic, diagnostic, or epidemiological), ensuring that surveillance workflows maintain high standards for data integrity, provenance, and security.
• Influence the technical roadmap and long-term evolution of the Biosecurity platform, identifying and mitigating technical debt and architectural bottlenecks before they impact delivery.
• Design and implement robust CI/CD pipelines where automated unit, integration, and security testing are treated as mandatory gates for every code deployment.
• Drive engineering excellence by leading technical design reviews and providing critical feedback on software modularity, while upholding rigorous standards for documentation, observability, and long-term maintainability
• Support production systems by monitoring performance, troubleshooting issues, and continuously improving reliability, including on-call support and triage in off hours

Minimum Requirements

• 6-8+ years of professional software engineering experience, with significant full-stack development work, including ownership of complex systems and cross-team technical initiatives.
• Strong proficiency in Python for backend development (our primary programming language).
• Experience building and consuming APIs (REST and/or GraphQL).
• Experience developing modern web frontends using JavaScript/TypeScript and frameworks such as React.
• Demonstrated ability to integrate AI-assisted development tools (e.g., GitHub Copilot, Cursor, or similar) into daily workflows to increase productivity and code reliability
• Proven experience collaborating  domain experts (scientific, operations, product, etc) to translate complex biological data (genomic, diagnostic, or epidemiological) into robust software solutions and actionable insights
• Solid grounding in software engineering fundamentals: data structures, system design, version control, and modern CI/CD patterns for automated testing and deployment

Preferred Capabilities and Experience

• Prior experience in bioinformatics, computational biology, public health, or a related domain.
• Familiarity with cloud infrastructure (e.g., AWS) and containerized environments (Docker, Kubernetes).
• Experience with data pipelines, workflow orchestration, or analytics platforms.
• Exposure to regulated or sensitive-data environments (e.g., HIPAA, public health data).
• Demonstrate high levels of ownership and independent execution
• Comfort working in fast-moving, ambiguous problem spaces where requirements evolve
• Flexibility and willingness to work on the highest priority needs of the business