Protein ML Senior Principal Data Scientist

Sanofi; Waltham (MA); On-site; USD 180,000 - 240,000; Full time

Job summary

Sanofi is seeking a Protein ML Senior Principal Data Scientist in Waltham, MA to design and deploy advanced ML models predicting protein properties for vaccine development. You’ll work at the interface of computational and bench sciences, leveraging protein language models to accelerate candidate selection and improve manufacturability.

You will mentor colleagues, collaborate with structural biology and design teams, and ensure robust, well-documented modeling practices while communicating

Qualifications

• PhD in Computational Biology, Data Science, Applied Mathematics, Biophysics or closely related field.
• 2+ years of industry or academia experience.
• Fluent English.
• Proficiency in Python, R and SQL; PyTorch experience.

Responsibilities

• Develop protein property prediction models for immunogenicity, stability, and manufacturability.
• Refine protein representations to accelerate vaccine candidate design.
• Analyze protein sequences, structures, and data to learn generalizable representations.
• Collaborate with biology and bench teams to guide modeling strategy and improve model quality.
• Maintain robust, reproducible modeling code and documentation.
• Mentor colleagues on protein modeling tools and techniques.
• Communicate findings clearly to internal and external stakeholders.

Skills

Python

R

SQL

PyTorch

AI-based modeling

Protein language models

Communication

Mentoring

Collaboration

Problem solving

Education

PhD in Computational Biology or related field

Tools

AlphaFold

OpenFold

Boltz

ESM

Claude Code

Job description

Job Title: Protein ML Senior Principal Data Scientist

Location: Waltham, MA

About The Job

As Protein ML Senior Principal Data Scientist within our Vaccines R&D Data and Computational Sciences team, you'll design and deploy state-of-the-art machine learning models that predict protein properties and accelerate the development of next-generation vaccines. Ready to get started?

In this role, you will harness the power of protein language models and foundational AI to predict immunogenicity, stability, and manufacturability - properties that are critical to bringing safe, effective vaccines to the world. Working at the interface of computational and experimental science, you will collaborate closely with antigen design and bench lab teams to iteratively refine protein property predictors and translate computational insights into real-world vaccine candidates.

Join the team protecting half a billion lives every year with next-gen science, mRNA innovation, and AI-driven breakthroughs. In Vaccines, you'll help advance prevention on a global scale - and shape the future of immunization.

About Sanofi

We're an R&D-driven, AI-powered biopharma company committed to improving people's lives and delivering compelling growth. Our deep understanding of the immune system - and innovative pipeline - enables us to invent medicines and vaccines that treat and protect millions of people around the world. Together, we chase the miracles of science to improve people's lives.

Main Responsibilities

• Develop state-of-the-art protein property prediction models with a focus on immunogenicity, stability, and manufacturability to support vaccine design.
• Leverage and refine language-based foundational protein representations to accelerate the identification and optimization of vaccine candidates.
• Analyze complex 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 the strategy for protein modeling and to iteratively improve model quality
• Maintain the modeling codebase according to best coding practices, ensuring results are robust, reproducible, and well-documented.
• Mentor and upskill colleagues on the latest advances in protein modeling tools and techniques, fostering a culture of continuous learning and scientific rigor.
• Communicate scientific findings clearly and compellingly to a broad range of internal and external stakeholders, adapting the level of detail to each audience.

About You

Education

• PhD degree in Computational Biology, Data Science, Applied Mathematics, Biophysics or a closely related field

Experience

• 2 + years of industry or academic setting experience.

Preferred Qualifications

• Exceptional track record in computational biology, encompassing protein language models, biophysics, and the development of AI-based predictive models; prior experience with immunogenicity predictors is a plus.
• Advanced proficiency in Python, R, and SQL, with hands‑on experience in 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 is an advantage.
• Familiarity with agentic tools such as Claude Code for automated software engineering strongly preferred.
• Demonstrated ability to communicate fluently - in writing and in person - across computational and bench lab teams, adapting messaging to diverse audiences including senior leadership
• Proven ability to mentor junior colleagues and lead collaboratively in the area of protein modeling.
• Strong problem‑solving, communication, and collaboration skills across multidisciplinary teams.

Language

• Fluent English required.

Why choose us?

• Bring the miracles of science to life alongside a supportive, future focused team.
• Discover endless opportunities to grow your talent and drive your career, whether it’s through a promotion or lateral move, at home or internationally.
• Enjoy a thoughtful, well‑crafted rewards package that recognizes your contribution and amplifies your impact.
• Take good care of yourself and your family, with a wide range of health and wellbeing benefits including high‑quality healthcare, prevention and wellness programs and at least 14 weeks' gender‑neutral parental leave.
• Work at the forefront of AI‑driven research, smart manufacturing, and groundbreaking mRNA platforms that are redefining the future of immunology.
• Help protect half a billion people every year, contributing to one of the largest global vaccination efforts in healthcare.
• Develop your career with access to mentoring, international mobility programs, and opportunities to grow across four continents.

Sanofi US Services and its U.S. affiliates are Equal Opportunity employers committed to a culturally inclusive workforce. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; marital, domestic partnership or civil union status; sex, gender, gender identity or expression; affectional or sexual orientation; disability; veteran or military status or liability for military status; domestic violence victim status; atypical cellular or blood trait; genetic information (including the refusal to submit to genetic testing) or any other characteristic protected by law.

All compensation will be determined commensurate with demonstrated experience. Employees may be eligible to participate in Company employee benefit programs, and additional benefits information can be found here.