Bioinformatics Platform Engineer

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.

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

About the Role

We are seeking a Bioinformatics Platform Engineer to join our Bioinformatics and Cloud Platform team. This is a highly hands-on role focused on operating, improving, and scaling the scientific computing infrastructure that powers production bioinformatics workflows. 

You 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. 

You will ramp up on our platform while actively contributing to its operation and improvement. As you gain familiarity, you will take on increasingly complex challenges — including solution architecting to support new bioinformatics workflows and enhancing platform capabilities. 

This role spans multiple layers of the platform, from infrastructure to bioinformatics workflows, and is well-suited for engineers who enjoy working across system boundaries. You’ll collaborate closely with scientists and engineers, contributing wherever needed to keep the platform running smoothly and evolving. 

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. 

What You’ll Do

• Operate and improve our 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 

Required Qualifications

• MS in Science, Engineering, Bioinformatics, Computational Biology, or related field 

• 3 years of experience working in pharma, biotech, or life sciences 

• Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.

Preferred Qualifications 

• Hands-on experience working with NGS and bioinformatics workflows languages (Nextflow, Snakemake) 

• Strong Linux systems expertise 

• Strong AWS experience, including IAM, EC2, S3, networking fundamentals 

• Experience with terraform, chef, or cloudformation

• 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 DevOps practices (Jenkins, GitHub 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 

What Success Looks Like 

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 

Cultural Fit 

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 dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

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 protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.  The anticipated wage for this position is

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

#WeAreLilly