Eli Lilly and Company · 2 months ago
Machine Learning Scientist/Sr Scientist - Antibody Property Prediction & Generative Design
US, Boston MA
Full-time
Onsite
Mid, Senior Level
$152K/yr - $244K/yr
2+ years expEli Lilly and Company is a global healthcare leader headquartered in Indianapolis, Indiana, dedicated to making life better for people around the world. The Machine Learning Scientist/Sr Scientist will specialize in antibody and biologic drug development, focusing on building AI models that accelerate antibody discovery and optimization through advanced machine learning techniques.
BiotechnologyHealth CareMedicalPharmaceutical
Responsibilities
Build multi-task learning frameworks specifically for antibody properties including binding affinity, specificity, stability (thermal, pH, aggregation), immunogenicity, and developability metrics from sequence and structural features
Develop and implement generative models (transformers, diffusion models, evolutionary models) for antibody design, including CDR optimization, humanization, and affinity maturation while maintaining structural integrity
Integrate structural modeling and prediction (AlphaFold, ESMFold) with generative approaches to ensure generated antibodies maintain proper folding, CDR loop conformations, and epitope recognition
Create models that simultaneously optimize for multiple developability criteria including expression yield, solubility, viscosity, and post-translational modifications, crucial for manufacturing and formulation
Develop approaches to design antibodies with desired species cross-reactivity profiles for preclinical development, learning from cross-species binding data
Create models for predicting antibody-antigen interactions, epitope mapping, and paratope design, incorporating both sequence and structural information
Qualification
Required
PhD in Computational Biology, Protein Engineering, Immunology, Biochemistry, or related field from an accredited college or university
Minimum of 2 years of experience in antibody or protein therapeutic development within the biopharmaceutical industry
Strong experience with protein sequence analysis and structural biology
Proven track record in machine learning applications to biological sequences
Deep understanding of antibody structure-function relationships and immunology
Preferred
Experience with immune repertoire sequencing and analysis
Publications on antibody design, protein engineering, or therapeutic development
Expertise in protein language models and transformer architectures
Knowledge of antibody manufacturing and CMC considerations
Experience with display technologies (phage, yeast, mammalian)
Understanding of clinical immunogenicity and prediction methods
Proficiency in protein modeling tools (Rosetta, MOE, Schrodinger BioLuminate)
Familiarity with antibody-drug conjugates and bispecific platforms
Experience with federated learning in biological applications
Portfolio mindset balancing innovation with practical developability
Benefits
Company bonus
Company-sponsored 401(k)
Pension
Vacation benefits
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)
Company
Eli Lilly and Company
We're a medicine company turning science into healing to make life better for people around the world.
10001+ employees
H1B Sponsorship
Eli Lilly and Company has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (514)
2024 (236)
2023 (167)
2022 (133)
2021 (57)
2020 (52)
Funding
Current Stage
Public CompanyTotal Funding
$6.5M2024-02-12Post Ipo Debt· $6.5M
1978-01-13IPO
Leadership Team
David Ricks
Chair, CEO
Lucas Montarce
Executive Vice President and Chief Financial Officer
Recent News
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2026-01-19
Pharmaceutical Technology
2026-01-19
2026-01-18
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