Software Engineer, AI & Clinical Applications

Eli Lilly and Company • Indianapolis, IN

2d • Hybrid

About The Position

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. Lilly is on a mission to transform medicine, and technology is at the heart of that transformation. As a Full-Stack Developer within Lilly's Medicines Development organization, you will engineer the platforms, tools, and applications that power Lilly's global clinical research efforts, with a primary focus on the Statistics and Clinical organizations. You will work at the intersection of data, science, and software, partnering with statisticians, clinical scientists, and regulatory professionals to deliver high-quality, compliant solutions that accelerate drug development worldwide. A central part of this role is designing and building AI-powered and agentic applications that automate complex clinical workflows, augment scientific decision-making, and modernize how Lilly's research teams operate at scale. This is a high-impact role for an engineer who is energized by the frontier of applied AI, excited by the complexity of regulated clinical computing environments, and motivated by the opportunity to directly improve patient outcomes.

Requirements

• Bachelor's degree in Computer Science, Software Engineering, Information Systems, or a related technical field.
• 3+ years of full-stack software development experience with production-deployed applications.
• Strong proficiency in Python for backend development and data processing.
• Demonstrated ability to collaborate across cross-functional teams, including non-technical scientific or clinical stakeholders.
• Excellent communication skills, with experience translating complex technical concepts for diverse audiences.
• As part of the interview process, you may be required to showcase your coding and problem-solving skills by completing a CoderPad exercise.

Nice To Haves

• Languages Python (primary), JavaScript/TypeScript, SQL; familiarity with R a plus
• AI & Agentic Hands-on experience building LLM-integrated applications; familiarity with agentic frameworks (e.g., LangChain, LangGraph, AutoGen, or MCP); prompt engineering; RAG architecture; responsible AI principles
• Frontend React or Vue.js; responsive UI design; data visualization libraries (e.g., Plotly, D3.js)
• Backend RESTful API design; FastAPI or Flask; Node.js; GraphQL
• Data & Pipelines Pandas, NumPy, PySpark; ETL/ELT pipeline development; familiarity with clinical data standards (CDISC SDTM, ADaM)
• Cloud & DevOps AWS or Azure; Docker; CI/CD pipelines; Git/version control
• Databases PostgreSQL, SQL Server, or Oracle; working knowledge of both relational and NoSQL data stores
• Security & Compliance Experience in regulated or GxP environments; understanding of audit trails, electronic signatures, and data integrity principles (21 CFR Part 11)
• Prior experience in a clinical, pharmaceutical, or life sciences technology environment.
• Exposure to statistical software environments such as SAS or SAS Viya, and awareness of SAS-to-open-source migration patterns.
• Familiarity with clinical trial data standards (CDISC, SDTM, ADaM) and regulatory submission processes.
• Experience building AI-assisted or agentic workflows, including LLM integrations or MCP-based architectures.
• Knowledge of ServiceNow or similar ITSM platforms within a GxP-compliant organization.

Responsibilities

• Own capabilities from concept to production, partnering with business stakeholders to shape requirements, driving delivery through cross-functional teams, and ensuring solutions are adopted and sustained in a regulated environment
• Design, develop, and maintain full-stack applications that support clinical trial data workflows, statistical computing, and regulatory reporting pipelines.
• Architect and build AI-powered and agentic applications, including LLM-integrated tools, multi-step autonomous agents, and MCP-based workflows that automate high-complexity tasks across the clinical and statistics organizations.
• Collaborate closely with global statisticians and clinical data scientists to translate analytical requirements into robust, scalable software solutions, surfacing AI capabilities that meaningfully reduce manual effort.
• Build and extend integrations across Lilly's clinical data ecosystem, including platforms such as CLUWE (Clinical Trial Data Platform), statistical computing environments (SCE), and downstream regulatory submission tooling.
• Develop APIs, microservices, and data processing pipelines that handle sensitive clinical data in compliance with 21 CFR Part 11, GxP standards, and Lilly data governance policies, including AI systems operating in those environments.
• Partner with DevOps and cloud engineering teams to deploy and maintain applications, including agentic systems, on enterprise cloud infrastructure.
• Participate in Agile ceremonies, contribute to product roadmaps, and continuously improve engineering practices, code quality, and documentation.
• Stay current on the rapidly evolving AI and agentic landscape, evaluating new frameworks and patterns that can be responsibly applied within Lilly's regulated development environment.
• Serve as a trusted technology partner to clinical and statistics leadership, translating complex technical concepts into clear business value and actively contributing to roadmap prioritization, resource planning, and stakeholder alignment.

Benefits

• company bonus (depending, in part, on company and individual performance)
• 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
• well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level