Bioinformatics Platform Engineer
Eli Lilly and Company, San Francisco, CA, United States
Overview
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 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 put people first and seek colleagues 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 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.
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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 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 put people first and seek colleagues 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 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.
#J-18808-Ljbffr