Biomedical Engineering Research Jobs in Indiana (NOW HIRING)

Job Summary:
Eli Lilly and Company is a global healthcare leader headquartered in Indianapolis, Indiana, focused on discovering and bringing life-changing medicines to those in need. They are seeking an experienced Product Management leader to shape the strategy and development of custom software platforms for discovery research, particularly in computational drug design and optimization for large molecules.
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
Qualifications:
Required:
• 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
Preferred:
• 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
Company:
We're a medicine company turning science into healing to make life better for people around the world. Founded in 1876, the company is headquartered in Indianapolis, USA, with a team of 10001+ employees. The company is currently Late Stage.