Software Engineer, Oncology Applications

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us. 

Position: Software Engineer, Oncology Applications
Reporting to: Director, Software Engineering
Location: San Diego, CA or South San Francisco, CA

About the Job

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.

Position Summary

Oncology at Lilly depends on software that connects people, data, systems, and workflows across research and business operations. The Software Engineer, Oncology Applications designs, builds, integrates, and sustains applications that improve access to information, reduce manual work, and help teams operate more efficiently.

The position sits within the software engineering group and serves the Oncology organization broadly. The engineer will partner with discovery and translational teams, scientific platforms, informatics, research operations, and Tech@Lilly. Work may include scientific data applications, workflow and process tools, dashboards and reporting, system integrations, automation, and AI-enabled interfaces. The portfolio will evolve with Oncology priorities and technologies.

The role requires sound engineering practices, thoughtful use of AI-assisted development, and a focus on secure, tested, maintainable systems.

Key Responsibilities

• Design, build, deploy, and sustain full-stack applications, data services, workflow tools, and automation for scientific and operational users.

• Partner with scientists, engineers, informatics teams, and business stakeholders to identify needs, clarify requirements, and define practical deliverables.

• Improve efficiency by simplifying processes, reducing manual handoffs and duplicative data entry, and connecting fragmented data and systems.

• Build and maintain APIs, data models, and access layers across scientific, operational, enterprise, and vendor data sources.

• Integrate applications with laboratory systems, data pipelines, analysis environments, and enterprise platforms.

• Apply appropriate standards for data quality, provenance, versioning, security, and access control.

• Develop AI-enabled capabilities where they provide clear value, such as information retrieval, natural-language data access, extraction, annotation, and summarization.

• Use AI-assisted development tools while maintaining established standards for code review, testing, security, and ownership.

• Evaluate technology options and recommend whether needs are best addressed through custom development, configuration, integration, reuse, purchase, process change, or retirement.

• Contribute to shared engineering practices, including version control, peer review, automated testing, CI/CD, containerization, observability, and dependency management.

• Deploy and operate applications on Lilly cloud infrastructure in partnership with Tech@Lilly and Information Security.

• Own application reliability, user support, documentation, maintenance, and lifecycle planning.

• Mentor junior engineers, co-ops, and scientist-developers as appropriate.

Required Qualifications

• BS or MS in computer science, software engineering, or a related discipline, with 5 or more years of professional software engineering experience. An equivalent combination of education and demonstrated experience will be considered

Additional Preferred Qualifications

• Strong programming experience with Python or another modern server-side language; Python experience is preferred.

• Experience developing web applications or APIs using modern server-side frameworks (preferred frameworks for experience: Django, Flask, Ruby on Rails)

• Front-end development experience with JavaScript or TypeScript and a modern component framework.

• Experience with relational database design, SQL, APIs, and system integration.

• Experience with cloud deployment, preferably AWS, as well as containerization and CI/CD pipelines.

• Fluency with Git-based collaborative development, code review, automated testing, and production support.

• Experience with AI-assisted development tools and working familiarity with LLM APIs or related application patterns.

• Ability to work directly with scientific and operational stakeholders and communicate technical options clearly to non-engineers.

• Demonstrated ability to work independently, manage concurrent projects, and adapt to changing priorities.

• Experience developing scientific, operational, or data-intensive business applications.

• Prior work in pharma, biotech, healthcare, research, or another regulated environment.

• Experience with biological data, laboratory systems, scientific instruments, or research data pipelines.

• Experience with workflow automation, enterprise integration, reporting, or interactive data visualization.

• Experience developing AI-enabled or agentic applications over internal data sources.

• Familiarity with data governance, sensitive-data handling, or controlled-access systems.

Work Environment and Physical Demands

This position is primarily computational and office-based, with regular in-person collaboration with laboratory, informatics, technology, and operations teams. Travel requirements are less than 5%. The physical demands described are representative of those required to perform the essential functions of this role. Reasonable accommodations may be made for individuals with disabilities.

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 (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

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.

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