Co-Founder or Founding Scientist – AI/ML Guided Protein Engineering

Helix BioSearch; Boston (MA); On-site; USD 200,000 - 300,000; Full time

Benefits offered by this job

Meaningful equity

Job summary

Helix BioSearch is seeking a Co-Founder or Founding Scientist to build an AI-native immunotherapy discovery platform from the ground up in collaboration with a stealth-mode biotech partner.

You will lead computational strategies for antibody/TCR design, sequence optimization and structure-function prediction, translating insights into experimental designs and shaping the platform’s technical roadmap.

Qualifications

• PhD or equivalent research experience in ML, computational biology, bioinformatics, CS, protein engineering, structural biology or related field.
• At least 2 years of industry or postdoc experience; open to early-career scientists to senior leaders.
• Hands-on experience applying AI/ML to biological problems.
• Strong understanding of protein engineering (CARs, antibodies, TCRs or related) and experience with sequence/structure data.
• Experience with protein language models, generative models, deep learning, representation learning, sequence optimization or structure-based modeling.
• Strong programming skills in Python and modern ML frameworks.

Responsibilities

• Develop and apply machine learning and AI models for therapeutic protein engineering and discovery.
• Work with biological sequence and structural data to build predictive and generative protein design approaches.
• Apply computational methods to antibody, TCR or related biologic engineering.
• Develop models for sequence-function relationships, affinity, specificity, developability, immunogenicity and other properties.
• Partner with experimental scientists to translate predictions into designs.
• Establish the company’s AI/ML and computational protein engineering strategy.
• Evaluate emerging advances in generative AI, protein language models, structure prediction and related tech.
• Contribute to the design of the computational platform and scientific roadmap.
• Help shape future hiring and research priorities as an early scientific leader.

Skills

PhD expertise

ML model development

Protein engineering

Python programming

Cross-functional leadership

Education

PhD or equivalent

Tools

Python

ML frameworks

Sequence data tools

Job description

Compensation: Founder Salary + meaningful equity

Build an AI-Native Immunotherapy Discovery Platform from the Ground Up

Helix BioSearch is partnering with a stealth-mode biotechnology company being built around an AI-native approach to the discovery and development of next-generation biologic immunotherapies. The company’s ambition is to use modern AI and machine learning as a fundamental part of the therapeutic discovery process, transforming how therapeutic proteins are designed, optimized and developed rather than simply adding computational tools to a conventional biotech workflow.

We are seeking a Co-Founder or Founding Scientist to join at a genuinely formative stage and help shape the company’s scientific and computational direction. This is a highly visible opportunity for a hands-on computational scientist who wants to go beyond applying established models – someone who wants to decide which problems should be solved, which approaches are most promising and how an AI-native discovery platform should be built.

Working closely with the founding team and experimental scientists, you will develop and apply computational approaches across antibody and/or T-cell receptor (TCR) engineering, sequence design, protein representation, structure-function prediction and optimization, translating computational insight into experimentally testable designs.

Key Responsibilities

• Develop and apply machine learning and AI models for therapeutic protein engineering and discovery.
• Work with biological sequence and structural data to build predictive and generative approaches for protein design.
• Apply computational approaches to antibody, TCR or related biologic engineering.
• Develop models for sequence-function relationships, affinity, specificity, developability, immunogenicity and other relevant protein properties.
• Partner closely with experimental scientists to translate computational predictions into experimentally testable designs.
• Establish the company’s AI/ML and computational protein engineering strategy.
• Evaluate and incorporate emerging advances in generative AI, protein language models, structure prediction and related technologies.
• Contribute to the design of the company’s underlying computational platform and scientific roadmap.
• Shape future hiring, research priorities and the broader technical direction of the company as an early scientific leader.

What We’re Looking For

• A PhD or equivalent research experience in machine learning, computational biology, bioinformatics, computer science, protein engineering, structural biology or a related field.
• A minimum of 2 years of industry or postdoctoral experience; candidates ranging from early-career scientists through to more senior computational scientists and technical leaders are welcome.
• Hands-on experience developing or applying AI/ML models to biological problems.
• A strong understanding of protein engineering, particularly CARs, antibodies, TCRs or other therapeutic proteins.
• Experience working with biological sequence and/or structural data.
• Experience with protein language models, generative models, deep learning, representation learning, sequence optimization or structure-based modeling.
• Strong programming skills, particularly in Python and modern ML frameworks.
• The ability to work effectively across computational and experimental biology.
• A desire to take significant ownership of a scientific platform and grow into a broader technical and scientific leadership role.

Why Apply?

• Meaningful equity in a founding-stage company
• Work directly with the founding team and help shape the company’s technical direction
• Significant opportunity for scientific and organizational impact
• Scope to grow into a broader technical/scientific leadership role as the company develops

This is an opportunity to join an AI-native biotech early enough to build the roadmap rather than inherit one. You’ll play a pivotal role in defining the company’s computational platform, scientific strategy and, ultimately, its direction.

If you’re passionate about machine learning, therapeutic protein design and building an AI-first discovery platform from the ground up, we’d welcome a confidential conversation.