Bioinformatics Platform Engineer

Location: San Francisco, CA | Indianapolis, IN | Boston, MA | San Diego, CA | New York, NY

We are seeking a Bioinformatics Platform Engineer to join our Bioinformatics and Cloud Platform team. This highly hands‑on role focuses on operating, improving, and scaling the scientific computing infrastructure that powers production bioinformatics workflows. The successful candidate will work at the intersection of bioinformatics, cloud infrastructure, and platform engineering, helping scientists run complex next‑generation sequencing (NGS) workflows reliably and at scale in AWS.

Over time, you will develop deep expertise in the platform, take ownership of key infrastructure components, and help shape the long‑term architecture of our scientific computing environment.

• Operate and improve the cloud platform that runs production NGS and bioinformatics workflows
• Support and troubleshoot scientific workflow pipelines (Nextflow preferred)
• Operate and debug Linux‑based production environments
• Investigate and resolve complex issues across the entire platform stack, including workflow orchestration, cloud compute and storage, networking and security, IAM, and application services
• Partner with scientists to translate workflow needs into scalable, secure platform solutions
• Contribute to infrastructure automation and platform reliability improvements
• Integrate and operate multiple research and enterprise platforms
• Apply cloud security and operational best practices
• Participate in technical roadmap discussions and platform architecture decisions

• MS in Science, Engineering, Bioinformatics, Computational Biology, or a related field
• 3 years of experience working in pharma, biotech, or life sciences
• Authorized to work in the United States on a full‑time basis (no sponsorship for work visa)

• Hands‑on experience with NGS and bioinformatics workflow languages (Nextflow, Snakemake)
• Strong Linux systems expertise
• Strong AWS experience, including IAM, EC2, S3, and networking fundamentals
• Experience with Terraform, Chef, or Cloud Formation
• Experience integrating systems across cloud and enterprise environments
• Demonstrated ability to debug complex systems spanning multiple technologies
• Ability to work independently and take ownership of problems
• Demonstrated ability to learn new technologies quickly and work across unfamiliar systems
• Experience with orchestrating and scaling scientific or data workflows in cloud or on‑prem environments
• Experience with infrastructure as code or automation tools to manage compute, storage, and networking resources
• Familiarity with data engineering, distributed compute, or high‑throughput analysis platforms
• Experience supporting collaborative data science or research environments
• Exposure to CI/CD pipelines and modern Dev Ops practices (Jenkins, Git Hub Actions)
• Experience developing or implementing testing frameworks for pipelines, workflows, or infrastructure
• Experience integrating with enterprise platforms, internal tools, or regulated systems
• Comfortable learning new tools and platforms quickly, adapting to changing environments, and working across multiple technologies

Within the first year you will:

• Gain a deep understanding of our scientific computing environment
• Become a trusted technical partner to scientists and engineers
• Independently support and troubleshoot production bioinformatics workflows
• Take ownership of key platform components
• Contribute meaningfully to architecture discussions and long‑term platform direction

We value engineers who are:

• Collaborative and easy to work with
• Comfortable navigating technical disagreement constructively
• Calm under pressure and solutions‑oriented
• Comfortable working across disciplines and stepping in wherever the team needs help
• Self‑driven and accountable
• Invested in team success and shared learning

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally…