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.

Director, Software Product Management – Discovery Research Platforms

Software Product Engineering Overview

Software Product Engineering builds and maintains capabilities using pioneering technologies like most prominent tech companies. What differentiates Software Product Engineering is that we create new possibilities through tech to advance Lilly’s purpose – creating medicines that make life better for people around the world, like model-driven drug discovery and connected clinical trials. We hire the best technology professionals from a variety of backgrounds, so they can bring an assortment of knowledge, skills, and diverse thinking to deliver innovative solutions in every area of our business.

Position Description

Eli Lilly is seeking an experienced Product Management leader to help shape the strategy and development of custom software platforms supporting discovery research, with a primary focus on computational drug design and optimization for large molecules.

You will be part of a cross-functional product area alongside engineering, computational biology, and research stakeholders – collaborating to build sophisticated systems that orchestrate multi-objective optimization workflows, integrate data from Next Generation Sequencing (NGS), high-throughput assays, and in silico modeling, and bring agentic AI capabilities into the hands of discovery scientists.

A key dimension of this role is helping to define how AI agents and intelligent automation can transform discovery research – from accelerating design-make-test-learn cycles in biologics optimization to enabling scientists to compose and execute complex computational pipelines through intuitive, AI-assisted interfaces.

You will partner closely with computational biologists, protein engineers, and engineering teams to translate these possibilities into production-ready capabilities. This role seeks both domain fluency in medicine discovery and the product skills to contribute to a multi-year roadmap, influence investment decisions, and drive adoption across discovery research.

The successful candidate will operate at the intersection of science, engineering, and business – translating complex research needs into scalable software platforms that accelerate Lilly’s biologics pipeline. While the initial focus is on computational drug design and optimization for large molecules, there are natural opportunities to broaden impact across adjacent lab and research platform areas over time.

The strong preference is for the role to be based in Indianapolis, though may consider San Diego as well, with periodic travel (approximately 30%) between sites to maintain close partnerships with research stakeholders and engineering teams in both locations.

Primary Position Responsibilities

Product strategy for computational drug design & optimization (40%)

• Contribute to and help drive the product strategy, roadmap, and vision for computational drug design and optimization platforms, translating scientific research objectives into a coherent product direction that aligns with Lilly’s broader discovery and AI strategies
• Deeply understand how computational biologists design, execute, and iterate on multi-objective optimization (MOO) campaigns for therapeutic candidates, and translate those needs into platform capabilities that standardize and accelerate these workflows
• Identify and prioritize opportunities to integrate agentic AI capabilities into discovery workflows, including intelligent pipeline composition, automated experimental recommendations, and conversational interfaces for scientists to interact with complex computational systems
• Establish and track key metrics to measure product success, adoption, and scientific impact, using data to inform investment decisions and communicate value to leadership
• Explore adjacencies across broader lab and research platform areas where shared infrastructure, data integration, or agentic capabilities could extend the impact of the product area

Technical translation & engineering partnership (35%)

• Work as part of a cross-functional product team with engineering, computational biology, and research stakeholders to translate complex scientific requirements into clear product specifications and execution plans, requiring understanding of:
• Next Generation Sequencing (NGS) data structures, quality metrics, and bioinformatics pipeline architectures
• Protein structure prediction algorithms (AlphaFold, ESMFold) and molecular dynamics simulation principles
• High-throughput screening data analysis and dose-response modeling
• Vector database architectures for biological sequence similarity search
• Workflow orchestration patterns for multi-step computational pipelines across heterogeneous compute environments (cloud, GPU clusters, internal platforms)
• Guide the integration of AI/ML capabilities into drug design and optimization, including deep learning architectures for protein engineering, generative models for antibody sequence design, active learning strategies for experimental optimization, and multi-objective optimization for therapeutic candidate selection
• Help shape the platform’s approach to agentic capabilities – working with engineering to design systems where AI agents can assist scientists in composing workflows, interpreting results, and suggesting next experiments
• Assess technical feasibility and complexity when prioritizing features, working closely with engineering to understand implementation trade-offs and architectural implications
• Work closely with engineering teams to ensure high-quality, on-time delivery, actively unblocking teams by clarifying requirements, resolving ambiguity, and making priority decisions in real time

Cross-functional collaboration & stakeholder partnership (25%)

• Build and maintain strong partnerships with research scientists, protein engineers, computational biologists, lab automation teams, and research leadership across both Indianapolis and San Diego sites
• Champion user needs and experience while balancing technical feasibility and business value, applying user-centered design principles and scientific workflow analysis
• Drive product development using agile methodologies, ensuring regular delivery of high-value features through sprint planning, backlog prioritization, and stakeholder alignment
• Communicate progress, risks, and strategic direction to SPE leadership and broader Lilly stakeholders as part of the cross-functional product area
• Contribute to the growth of Lilly’s product management discipline through mentorship, community of practice participation, and sharing of best practices from the discovery research domain

Basic Qualifications

• Bachelor’s degree in bioinformatics, computational biology, computer science, biomedical engineering, or biochemistry/molecular biology with demonstrated computational coursework
• 10 years of progressive software product management experience with a proven track record of taking complex technical products from vision through launch and sustained adoption
• 5+ years of experience working in life sciences, laboratory environments, drug discovery, or biopharmaceutical research settings

Additional skills and preferences

• Demonstrated success driving product strategy and execution in complex, highly regulated organizational environments at a senior level
• Experience working within cross-functional product teams and influencing without direct authority across matrixed organizations
• Masters or Ph.D. in computational biology, bioinformatics, or related field
• Experience with scientific software platforms or research tools in pharmaceutical R&D
• Deep understanding of AI/ML applications in life sciences and therapeutic development, including emerging agentic and generative AI approaches
• Familiarity with computational drug design and optimization workflows, particularly multi-objective optimization for biologics
• Experience managing products in regulated environments (FDA, GxP)
• Track record of successful cross-functional collaboration in matrix organizations at senior levels
• Experience with Agile/Scrum methodologies and product management tools (Jira)
• Strong technical background with understanding of modern software development processes, cloud architectures, and API-driven systems
• Interest in and aptitude for working across adjacent research and lab platform domains as the portfolio evolves
• Willingness to travel 30–40% between Indianapolis and San Diego to maintain close stakeholder and team relationships

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 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 $162,000 - $268,400. 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