Deep Learning Scientist II, Protein Sciences

Repertoire Immune Medicines, Inc.; Watertown (MA); On-site; USD 150,000 - 170,000; Full time

Benefits offered by this job

Medical insurance

Dental insurance

Vision insurance

Life insurance

Flexible time off

401(k) plan

Bonus opportunities

Job summary

Repertoire Immune Medicines is seeking a Deep Learning Scientist II to accelerate discovery and development of transformative therapeutics, leveraging proprietary datasets on TCR-pMHC interactions. You will join the Artificial Immune Intelligence Team to design, train, and apply advanced AI methods to protein engineering challenges.

The role involves close collaboration with wet-lab scientists, focusing on model development, evaluation, and deployment within a fast-paced research environment.

Qualifications

• PhD in computer science, computational biology or a related quantitative field.
• 2-5 years of industry experience in protein engineering and design.
• Experience training and fine-tuning protein language models (PLMs) and structure-prediction models.
• Ability to reason about protein-protein interactions with physics-based methods and ML.
• Strong programming in Python with multi-GPU training.
• Experience modeling high-dimensional biological data.
• Experience with TCR-pMHC binding is a plus.
• Intellectual curiosity and fast-paced environment.

Responsibilities

• Develop deep learning approaches spanning protein language models, structural modeling, and multi-modal representation learning to reason about the TCR-pMHC synapse.
• Apply problem-appropriate machine learning, statistics, computational biology, and data science techniques, working closely with wet-lab scientists to understand assay technologies.

Skills

Python

Protein language models

Multi-GPU training

Deep learning

Education

PhD in CS

Computational Biology

Tools

Structure prediction models

Applied AI pipelines

Job description

Company Overview

Repertoire Immune Medicines is a clinical-stage biotechnology company harnessing the power of the human immune system to develop transformative therapies for cancer and autoimmune disease. Using its proprietary DECODETM platform—which maps the immune synapse between T cell receptors (TCRs) and their antigen targets—Repertoire translates unique biological insights into potent and targeted off-the shelf immune medicines. The company integrates deep protein engineering expertise with artificial intelligence, powered by a proprietary DECODE database of over one billion TCR-antigen interactions, to accelerate discovery and optimize drug candidates.

From its sites in Cambridge, Massachusetts and Zurich, Switzerland, Repertoire is advancing a pipeline of T cell-targeted immunotherapies with the potential to address a broad range of cancers and autoimmune disorders. The company’s lead oncology program, RPTR-1-201, a TCR bispecific, has initiated a Phase 1/2 clinical trial across multiple solid tumor indications. Repertoire plans to advance additional TCR bispecific therapies into clinical trials over the next 12-18 months. In autoimmune disease, Repertoire is partnering with leading pharmaceutical companies to develop mRNA tolerizing therapies designed to selectively expand regulatory T cells and reset the immune system.

Repertoire was founded in 2019 by Flagship Pioneering and is supported by a strong investor base. The DECODE platform has been validated through four strategic partnerships with leading pharmaceutical companies—Bristol Myers Squibb, Genentech, Eli Lilly, and Pfizer—representing over $4.5 billion in disclosed total deal value and $185 million in upfront payments received to date.

Role Overview

Repertoire Immune Medicines is seeking a Deep Learning Scientist II to join the Artificial Immune Intelligence Team to accelerate the discovery and development of transformative therapeutics, exploiting proprietary datasets about T cell receptors interacting with peptide-MHC complexes.

Key Responsibilities

• Develop novel deep learning approaches spanning protein language models, structural modeling, and multi-modal representation learning to reason about the TCR-pMHC synapse.
• Apply problem-appropriate machine learning, statistics, computational biology, and data science techniques, working closely with wet-lab scientists to understand assay technologies.

Qualifications/Experience

• PhD in computer science, computational biology or a related quantitative field, with 2-5 years of industry experience in protein engineering and design.
• Hands-on experience with training and fine-tuning protein language models (PLMs) and structure-prediction models, and in the development of applied AI pipelines for biological data.
• Ability to reason about protein-protein interactions through rational structure-based approaches, using physics-based methods and machine learning workflows.
• Strong programming skills in Python, including multi-GPU training with PyTorch and related libraries
• Proven ability to analyze and model complex, high-dimensional biological datasets using sound computational and statistical practices to drive novel insights.
• Experience working with TCR-pMHC binding is a strong plus.
• Intellectual curiosity, scientific rigor, and enthusiasm for working in a fast-paced, evolving research environment.

The base salary for this role ranges from $150,000 to $170,000 and is determined based on a candidate’s skills, experience, and internal equity. In addition to a competitive base salary, Repertoire offers a broad range of benefits designed to attract, retain, and motivate top talent, including medical, dental, vision, and life insurance, flexible time off, a 401(k) retirement plan, and short- and long-term incentive opportunities. Compensation and benefits are based on Repertoire’s good faith estimate at the time of publication and may be updated in the future.

Repertoire is committed towards social responsibility and developing an inclusive culture. Much as the power of the immune system lies in the diversity of T and B cells, we believe that our work requires the creativity and ingenuity of a diverse workforce, and we are committed to pursuing that in all facets of the work experience at Repertoire. We will continue to educate ourselves about the inequities and barriers present in our society and act as a company where we can make a difference.

Repertoire is proud to be an Equal Opportunity Employer.