Director, Generative Design & Optimization, Biotherapeutics

100 Eli Lilly and Company; San Diego (CA); On-site; USD 194,000 - 339,000; Full time

Benefits offered by this job

401(k)

Pension

Vacation benefits

Medical benefits

Job summary

Eli Lilly and Company in San Diego leads pioneering generative design and optimization for biotherapeutics. The role guides conditioning, sampling, scoring, and integration of design workflows across therapeutic discovery programs.

The position requires a PhD with a strong track record in computational molecular design, deep learning, and leadership of cross-disciplinary teams, with collaboration across model and validation groups.

Qualifications

• Ph.D. in a STEM field with 3+ years experience; or an M.S. with 6+ years; or a B.S. with 8+ years.
• Track record leading computational or generative molecular design efforts that resulted in experimentally evaluated designs.
• Expertise in designing and building training/evaluation datasets for sequence, structure, or molecular design models.
• Strong Python skills and experience with a modern deep learning framework and GPU computing.

Responsibilities

• Conditioning and controllable molecule design to steer designs toward epitope-specific antibodies.
• Sampling and optimization to maximize design quality and discovery efficiency.
• Scoring and ranking that combine learned and physics-based signals for design prioritization.
• Training corpus strategy with provenance, splits, and leakage controls.
• Build and scale integrated design pipelines across generation, sampling, optimization, scoring, and selection.

Skills

Generative design

Deep learning

Python

GPU computing

Leadership

Education

PhD in computer science or related STEM

MS with 6+ years of experience

BS with 8+ years of experience

Job description

Director, Generative Design & Optimization, Biotherapeutic

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. 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

• Conditioning and controllable molecule design. Lead the development of conditioning, guidance, and restraint methods that steer foundation-model output toward epitope-specific, structurally plausible antibody and VHH designs.
• Sampling and optimization. Devise the iterative optimization layer and sampling strategy that balances exploration and exploitation to maximize design quality, experimental success, and discovery efficiency.
• Scoring and selection. Lead the development of scoring and ranking methods that combine learned and physics-based signals so the pipeline reliably prioritizes designs based on binding affinity, functional performance, developability, and other therapeutically relevant properties.
• Training corpus strategy. Establish versioned training, fine-tuning, and evaluation corpora with documented provenance, structure-aware splits, composition analysis, and leakage controls. Leverage multimodal and proprietary biological data to create a differentiated advantage in molecular design.
• Build and scale integrated design pipelines. Develop and operationalize workflows spanning conditioned generation, sampling, optimization, scoring, diversity selection, and experimental test nomination that can be applied repeatedly across therapeutic discovery programs.
• Set performance evaluation. Establish metrics that connect computational design quality to experimental outcomes, therapeutic objectives, and downstream portfolio impact.
• Lead a high-performing team and provide scientific leadership. Set technical direction and priorities, recruit and develop scientists and engineers, establish technical standards, and deliver against committed milestones.
• Collaboration. Guide the team and work hand in hand with the Foundation Models and Active Learning & Design Validation teams to define how each pipeline component is benchmarked and tested against experimental evidence and translate those results into the next iteration.
• Evaluate and incorporate external innovation. Assess advances in generative biology, molecular optimization, active learning, and AI-enabled therapeutic design, determining when to build, adapt, or partner.
• Communicate scientific strategy and impact. Present technical progress, experimental validation, key learnings, and strategic recommendations to scientific leadership and broader R&D stakeholders.
• Contribute to publications, external collaborations, and scientific presentations where appropriate.

Basic Requirements

• Ph.D. in computer science, computational biology, bioengineering, chemistry, physics, or a related STEM discipline with 3+years of relevant experience; or an M.S. with 6+years; or a B.S. with 8+ years.
• Track record leading computational or generative molecular design efforts that resulted in experimentally evaluated molecular designs.
• Expertise in designing and building training or evaluation datasets for sequence, structure, or molecular design models.
• Strong Python skills and experience with a modern deep learning framework and GPU computing.

Additional Preferences

• Proven record in conditional generation, guided sampling, active learning, Bayesian optimization, multi-objective optimization, quality-diversity methods, or related molecular design approaches.
• Expertise in protein structure analysis and translating structural knowledge into model constraints, optimization objectives, or selection criteria.
• Expertise in sequence-identity-aware and structure-aware data splitting, benchmarking, and leakage assessment.
• Contribution to a de novo binder or antibody design effort that reached experimentally validated designs.
• Experience combining learned and physics-based signals in scoring, ranking, or optimization workflows for molecular designs.
• Experience mentoring scientists or engineers or leading a multi-person technical effort.
• Track record of productive collaboration in multidisciplinary teams spanning computational and experimental sciences.
• Ability to communicate across domains and explain design capabilities, opportunities, and limitations to non-computational colleague.

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 $193,500 - $338,800 Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).

Benefits

• 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
• 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 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!

#WeAreLilly