AI Protein Design Co-Op

Company Overview

Ampersand Biomedicines is an innovative, privately held biotechnology company leading the way in developing multi-specific medicines that direct a wide range of therapeutic molecules to specific cells and biological contexts (www.Ampersand.bio). Ampersand was founded in Flagship Pioneering’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA) and Seres Therapeutics (NASDAQ: MCRB) were conceived and created. With a strong emphasis on innovation, Ampersand cultivates a highly dynamic and entrepreneurial environment.

Position Summary
We are seeking a motivated and technically strong Co-op student to join Ampersand’s Computational Sciences team from January to June/July 2026. The co-op will focus on developing robust, modular pipelines to support antibody design, exploring emerging AI/ML tools, and ensuring code quality across our computational workflows. This position offers the opportunity to gain hands-on experience at the interface of machine learning, pipeline engineering, and computational biology, while contributing to cutting-edge biotech innovation. To facilitate interactions with other team members and to make the most significant impact on our scientific endeavors, this position requires full-time, on-site presence. 

Responsibilities

• Explore and benchmark emerging AI/ML methods for protein and antibody design.
• Support deployment and maintenance of antibody development workflows.
• Deploy machine learning method to promote antibody binder design.
• Consolidate and refactor existing scripts and workflows into modular, reproducible pipelines.
• Improve code robustness, testing, and documentation.
• Collaborate with experimental teams to advance antibody binder design.

Qualifications

• M.S. or Ph.D. candidate in Computer Science, Bioinformatics, Computational Biology, or related field.
• Minimum of 2 years coding experience, with strong proficiency in Python and Linux.
• At least one hands-on AI/ML project (academic, research, or applied).
• Familiarity with common tools and environments: PyTorch, AWS, and basic DevOps (e.g., GitHub Actions).
• Fundamental knowledge in life sciences coupled with a keen interest in computational protein design.
• Must be able to relocate to the office location and work 40hrs/week, Monday-Friday, for the full duration of the co-op

Preferred

• Experience with workflow tools (Snakemake, Nextflow) or cloud platforms.
• Familiarity with antibody structure/function.
• Publications, preprints, or contributions to open-source projects.
• Strong communication and collaboration skills in an interdisciplinary setting.