AVP, Generative Design & Optimization, Biotherapeutics

100 Eli Lilly and Company; San Diego (CA); On-site; USD 267,000 - 392,000; Full time

Benefits offered by this job

Bonus eligibility

401(k) plan

Health, dental, vision benefits

Job summary

Lilly Biotechnology Center in San Diego is seeking an AVP of Generative Design & Optimization to lead AI-driven biotherapeutics discovery. The role focuses on building a scalable design platform combining AI/ML, structure biology, and high-throughput experiments to create novel therapeutic antibodies and proteins.

Based in San Diego, the role drives end-to-end design pipelines, collaborates with discovery and automation teams, and shapes data strategy to accelerate therapeutic discovery while

Qualifications

• Ph.D. in computer science, computational biology, bioengineering, chemistry, physics, or a related STEM field.
• 5+ years post-Ph.D. research experience (or MS with 10+ years).
• At least 3 years of experience leading scientists or engineers as a formal people manager.
• Demonstrated experience leading computational or generative molecular design campaigns with experimental validation.
• Proficiency in Python and a modern deep learning framework, with working knowledge of GPU-based computing.

Responsibilities

• Advance generative molecule design and translate design intent into explicit computational specs.
• Define sampling, search, and scoring strategy to maximize design quality and portfolio impact.
• Lead multi-objective optimization across binding, kinetics, developability, and therapeutic attributes.
• Define data strategy to convert internal/external data into design-ready assets.
• Build end-to-end design pipelines spanning epitope definition to experimental nomination.
• Represent the organization as a scientific leader and drive cross-functional alignment.

Skills

Python programming

Deep learning

Team leadership

Education

PhD in STEM

MS with 10+ years experience

Tools

GPU-based computing

Deep learning framework

Job description

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.

AVP, Generative Design & Optimization, Biotherapeutics

At Lilly, we unite caring with discovery to make life better for people around the world. For more than 25 years, Lilly’s Biotechnology Discovery Research (BioTDR) organization has advanced novel antibody and peptide therapeutics from concept through clinical development to market in areas of high unmet medical need. This role is based at the Lilly Biotechnology Center in San Diego, where we are expanding our computational capabilities to build a generative design platform. By bringing together AI/ML, protein engineering, automation, structural biology, and high-throughput experimentation, BioTDR is creating an integrated de novo design platform capable of generating, ranking, and optimizing novel therapeutic antibodies and other biotherapeutics with improved activity, safety, manufacturability, and target coverage. Designs are rapidly evaluated through experimental validation, creating a continuous learning cycle that strengthens both models and discovery outcomes. The program is supported by dedicated capacity on LillyPod, our wholly owned 1,016‑GPU NVIDIA Blackwell Ultra SuperPOD. Help us push the de novo protein design frontier beyond binders to molecules that can become medicines, faster. Ready to make an impact? Join us.

Primary Responsibilities

• Advance controllable molecule generation. Translate therapeutic design intent into explicit computational design specifications. Develop approaches for intentional design against defined biological objectives including epitope, molecule format, and therapeutic attributes.
• Define sampling, search, and scoring strategy. Establish approaches that maximize design quality and portfolio impact, determining where increased exploration improves outcomes and where intelligent search provides greater efficiency than brute‑force scaling.
• Lead multi‑objective optimization. Establish Pareto‑based and constraint‑based optimization strategies spanning binding affinity, kinetics, specificity, functional activity, developability, immunogenicity, and other therapeutically relevant properties.
• Define data and corpus strategy. Determine how internal and external biological, structural, and experimental data are converted into design‑ready assets that accelerate model performance and therapeutic discovery. Training corpus content and sampling strategy will be jointly governed with the Foundation Models and Active Learning & Design Validation teams.
• Establish an end‑to‑end design pipeline. Build robust workflows spanning epitope definition, conditioned generation, sampling and search, scoring, optimization, diversity selection, and experimental nomination. Ensure workflows are scalable, reproducible, traceable, and adaptable across programs.
• Define success metrics and decision frameworks for generative design performance. Ensure progress is measured against experimental outcomes and therapeutic objectives rather than computational benchmarks alone.
• Build and lead a world‑class organization and provide cross‑functional leadership. Recruit, develop, and retain exceptional computational scientists and AI researchers. Establish the culture, technical standards, and talent strategy needed for long‑term success. Partner closely with biotherapeutics discovery, automation, experimental sciences, and computational leaders across Lilly to maximize portfolio impact.
• Evaluate emerging technologies and external innovation. Stay current with advances in generative AI, molecular design, optimization, active learning, and related technologies. Evaluate external methods, collaborations, and partnerships, and determine when to build, adapt, or partner.
• Represent the organization as a scientific leader. Serve as an internal and external thought leader in AI‑enabled biologics discovery, communicating scientific strategy and progress to senior leadership and representing the organization through publications, conferences, collaborations, and engagement with the broader scientific community.

Basic Requirements

• Ph.D. in computer science, computational biology, bioengineering, chemistry, physics, or a related STEM field, with 5+ years post‑Ph.D. research experience (or M.S. with 10+ years).
• At least 3 years of experience leading scientists or engineers as a formal people manager, including building or scaling a team.
• Demonstrated experience leading computational or generative molecular design campaigns that resulted in experimentally evaluated molecular designs.
• Demonstrated experience setting data strategy for molecular design models, including sourcing, integrating, and governing heterogeneous internal and external sequence, structure, and assay data.
• Proficiency in Python and a modern deep learning framework, with working knowledge of GPU‑based computing.

Additional Preferences

• Expertise in conditional generation, guided sampling, active learning, Bayesian optimization, multi‑objective optimization, quality‑diversity methods, or related approaches for molecular design.
• Expertise integrating learned and physics‑based scoring into molecular design workflows.
• Strong structural biology judgment, including the ability to translate epitope and interface information into model constraints, optimization objectives, or selection criteria.
• Expertise in antibody, VHH, peptide, or other therapeutic protein design.
• Experience establishing rigorous design, optimization, benchmarking, or evaluation frameworks adopted across research organizations or discovery programs.
• Experience collaborating effectively across computational and experimental disciplines.
• Excellent communication skills, including the ability to translate complex computational concepts for non‑computational scientists, influence senior scientific leaders, and drive cross‑functional alignment.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions.

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 $267,000 - $391,600. 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.

At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe!