Protein ML Senior Principal Data Scientist

Sanofi • Waltham, MA

9d • $148,500 - $214,500 • Onsite

About The Position

As a Protein ML Senior Principal Data Scientist on the Vaccines R&D Data and Computational Sciences team, you will design and deploy machine learning models that predict protein properties and accelerate development of next-generation vaccines. You will use protein language models and foundational AI to predict immunogenicity, stability, and manufacturability, working at the interface of computational and experimental science. In close collaboration with antigen design and bench lab teams, you will iteratively refine protein property predictors and translate computational insights into vaccine candidates.

The role also involves analyzing protein sequence, structure, and functional data to identify generalizable representations across vaccine programs; maintaining robust, reproducible, well-documented modeling code; mentoring colleagues; and communicating scientific findings to varied stakeholders. The position is based in Waltham, Massachusetts.

Requirements

• PhD in Computational Biology, Data Science, Applied Mathematics, Biophysics, or a closely related field.
• At least 2 years of experience in an industry or academic setting.
• Fluent English.
• Strong problem-solving, communication, and collaboration skills across multidisciplinary teams.

Nice To Haves

• Track record in computational biology, including protein language models, biophysics, and AI-based predictive model development; experience with immunogenicity predictors is a plus.
• Advanced proficiency in Python, R, and SQL, with hands-on experience using PyTorch and AI-based structural modeling tools such as AlphaFold, OpenFold, and Boltz.
• Deep knowledge of protein representation models such as ESM.
• Familiarity with molecular dynamics, next-generation sequencing analysis, and deep mutational scanning.
• Familiarity with agentic tools such as Claude Code for automated software engineering is strongly preferred.
• Ability to communicate across computational and bench lab teams and adapt messaging to audiences including senior leadership.
• Ability to mentor junior colleagues and lead collaboratively in protein modeling.

Responsibilities

• Develop protein property prediction models focused on immunogenicity, stability, and manufacturability to support vaccine design.
• Leverage and refine language-based foundational protein representations to accelerate identification and optimization of vaccine candidates.
• Analyze relationships between protein sequences, structures, and functional data to uncover generalizable representations applicable across vaccine programs.
• Collaborate with structural biology, protein design, and bench lab teams to shape protein modeling strategy and iteratively improve model quality.
• Maintain the modeling codebase using best coding practices and ensure results are robust, reproducible, and well-documented.
• Mentor and upskill colleagues on advances in protein modeling tools and techniques.
• Communicate scientific findings clearly to internal and external stakeholders, adapting the level of detail to the audience.

Benefits

• At least 14 weeks of gender-neutral parental leave.
• Health and wellbeing benefits, including healthcare, prevention, and wellness programs.
• Mentoring and international mobility programs, with opportunities to grow across four continents.
• Employee benefit programs; further information is available through the company.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree