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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.

The Biotechnology Discovery Research Division in San Diego plays a crucial role in generating, characterizing, and optimizing biotherapeutics, from hit generation through lead optimization and preclinical development. We support cross-disciplinary efforts to engineer innovative biotherapeutics that treat metabolic, autoimmune, oncologic, and neurologic diseases.

We are currently seeking a self-motivated, collaborative Machine Learning Scientist to drive ML/AI powered protein design for next-generation biologics, including antibody, protein, peptide and beyond. If you are an expert in machine learning and a relentless problem solver who shares our passion for making a difference, we invite you apply!

Responsibilities

• Design and implement cutting-edge algorithms, such as diffusion or LLM -based protein models, for de novo protein design.

• Develop in silico or de novo antibody discovery and engineering methods to enable challenging targets.

• Analyze diverse experimental data, identify gaps in model capabilities, and enhance the performance of the protein design pipeline.

• Evaluate and push the boundaries of state-of-the-art algorithms, particularly those related to protein design.

• Partner with experimental, computational scientists, and IT professionals to refine strategies for data generation and acquisition for ML trainings.

• Regularly share progress in internal and cross-functional research meetings. Additionally, actively engage with the external scientific community by contributing through publications and presentations.

Basic qualifications

• PhD in computational biology, computer science, bioinformatics, or a related discipline.

• Industry Experience developing and applying machine learning and AI algorithms addressing protein design and engineering problems of biological interest.

Preferred qualifications:

• Proficiency in programming languages/tools (Python or R).

• Hands-on experience with RosettaFold, RFdiffusion, AlphaFold, or ESM, ESMFold.

• Proficiency in protein modeling and design software, such as PyMOL, Rosetta, Schrodinger, Molecular Operating Environment (MOE).

• Strong publication record in protein design and engineering for therapeutic proteins. Experience with antibodies highly desired.

• Excellent written and oral communication skills, including an ability to explain complex ideas to partners (e.g. experimentalists, data scientists, and other computational scientists/IT professionals).

• Understand business requirements and effectively translate business needs and process into technical terms, and vice versa.

• Strong collaborative skills and proven ability to work with a cross-functional team.

Eli Lilly and Company, Lilly USA, LLC and our wholly owned subsidiaries (collectively “Lilly”) are committed to help individuals with disabilities to participate in the workforce and ensure equal opportunity to compete for jobs. If you require an accommodation to submit a resume for positions at Lilly, please email Lilly Human Resources ( LillyRecruitingCompliance@lists.lilly.com ) for further assistance. Please note This email address is intended for use only to request an accommodation as part of the application process. Any other correspondence will not receive a response.

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