Senior Machine Learning Research Engineer

The Role

Senior Machine Learning Research Engineer. As a Senior Machine Learning Research Engineer at Dyno Therapeutics, you will partner closely with our Machine Learning Research teams to design, develop, and optimize deep learning models for next-generation AAV capsid design. This role is deeply embedded in the research effort - focused on building, evaluating, and iterating on models that power our platform. You will bring engineering excellence to our ML research pipeline, helping scale our modeling impact and accelerate experimental design cycles.

Job Type: Full Time

Location: Watertown, MA or NYC (may consider remote candidates)

How You Will Contribute

As a Senior Machine Learning Research Engineer, you will collaborate with ML researchers to co-develop deep learning models, refine our experimental modeling workflows, and build high-leverage tools and data pipelines that increase team productivity. Your work will directly influence Dyno’s ability to generate and optimize novel capsids with therapeutic potential.

Responsibilities: 

• Work alongside ML researchers to design and train state-of-the-art models (e.g., generative models, classifiers, regressors) in PyTorch or JAX.
• Build research tooling to improve model development workflows—experiment tracking, evaluation metrics, and training diagnostics.
• Design, develop, and maintain scalable data pipelines for ML data from external (PDB, UniProt, etc.) and internal sources.
• Optimize training performance and model efficiency across diverse datasets and compute environments.
• Develop codebases that balance rapid iteration with long-term maintainability and clarity.
• Contribute to internal libraries for sequence modeling, data processing, augmentation, and featurization.
• Collaborate with domain scientists to understand modeling needs and experimental constraints.
• Stay current with new ML methodologies, evaluating emerging approaches for potential integration into Dyno’s platform.

Basic qualifications

• 2+ years of post-graduate, full-time work experience in ML-focused roles.
• Strong proficiency in Python, especially in ML and data science contexts.
• Experience with deep learning frameworks such as PyTorch or JAX.
• Familiarity with ML experiment tracking, model evaluation, and reproducibility best practices.
• Experience working with and building pipelines for scientific or structured datasets (e.g., sequences, graphs, tabular data).
• Alignment with Dyno’s core values.

Preferred qualifications

• Prior work in protein design, biological sequence modeling, or ML for biology.
• Experience developing generative models (e.g., LLMs, VAEs, diffusion models) or large-scale predictive models.
• Familiarity with training at scale using GPUs in cloud or HPC environments.
• Experience writing tools to support collaborative model development and review (e.g., dashboards, visualizations).
• Understanding of the biological context of sequence-function relationships.

The Company

At Dyno Therapeutics, we are a high-energy, high-impact team on a mission to build high-performance genetic technologies that transform patient lives. Our team unites world-class molecular biologists, protein engineers, software developers, data scientists, and machine learning experts—all working together at the intersection of AI and genetic medicine.

Our culture is defined by three core values that guide everything we do:

• One Mission: Everything we do is for the mission. We are a cohesive and motivated team, thinking ahead and supporting one another to overcome challenges.
• Proactive Responsibility: We take action, inject energy into our work, and hold ourselves accountable for delivering results.
• Reaching for Excellence: We constantly strive for excellence, fueled by curiosity, adaptability, and the courage to speak hard truths in pursuit of success.

These values are more than words—they drive our actions and decisions. Our greatest strength isn’t technology—it’s our work ethic. More than just technologists, we’re a team of relentlessly resourceful problem-solvers: with an unshakable drive we generate breakthroughs at the intersection of AI and genetic medicine.

🚀 What You’ll Give:

• Bring an unstoppable work ethic, stepping up when things get tough and adapting as priorities shift.
• Embrace challenges as opportunities, finding solutions where none exist and driving innovation forward.
• Operate with urgency, responsibility, and resilience, because this mission demands the best from us.

🎯 What You’ll Get:

• Competitive compensation & equity—your contributions drive results, and we pay accordingly.
• Mission-aligned, high-trust environment—we succeed together, supporting each other through challenges.
• A career-defining experience—work at the forefront of AI-driven genetic medicine, tackling problems that reshape healthcare.

If you’re ready to push boundaries, build the future, and thrive in a fast-moving, high-impact environment—we’d love to hear from you.

Equal Employment Opportunity (EEO) Statement

We are an equal opportunity employer and value diversity at our company. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.

Fraud Alert: Please be aware of recruitment scams targeting job seekers. Dyno Therapeutics will never make an offer of employment without conducting a formal interview process, nor will we ask for personal information such as financial details over email. Official communication will only come from an @dynotx.com email address. If you are contacted by someone claiming to represent Dyno Therapeutics from any other domain, please report it as spam and report the communication to us at jobs@dynotx.com.