AVP, Generative Design & Optimization, Biotherapeutics

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

Benefits offered by this job

Bonus program

401(k) plan

Comprehensive health benefits

Well-being benefits

Paid time off

Job summary

Lilly is seeking an AVP, Generative Design & Optimization for Biotherapeutics based at the Lilly Biotechnology Center in San Diego. You will lead the design of generative molecular design campaigns, coordinating AI, protein engineering, and automation to accelerate therapeutic discovery.

You will build and mentor a world-class computational sciences team, shape data strategies, and collaborate across discovery platforms to turn computational insights into medicines faster.

Qualifications

• 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.

Responsibilities

• Advance controllable molecule generation. Translate therapeutic design intent into explicit computational design specifications.
• Define sampling, search, and scoring strategy. Establish approaches that maximize design quality and portfolio impact.
• Lead multi-objective optimization. Establish Pareto-based and constraint-based optimization strategies across key therapeutic properties.
• Define data and corpus strategy. Convert internal/external data into design-ready assets to accelerate model performance.
• Establish end-to-end design pipeline spanning epitope definition, conditioned generation, sampling, scoring, optimization, and experimental nomination.
• Define success metrics and decision frameworks for generative design performance.
• Build and lead a world-class organization and provide cross-functional leadership across Lilly teams.
• Evaluate emerging technologies and external innovation; decide to build, adapt, or partner.
• Represent the organization as a scientific leader to senior leadership and external communities.

Skills

Python

Deep learning

GPU computing

Leadership

Molecular design

Education

Ph.D. in a related STEM field

MS with 10+ years

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. 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 $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.

#WeAreLilly