The Role
Develop deep learning methods for protein language modeling, structural modeling, and multimodal representation learning of TCR-pMHC interactions. Apply machine learning, statistics, computational biology, and data science to complex biological datasets while collaborating with wet-lab scientists. The role includes training and fine-tuning protein and structure-prediction models, building AI pipelines, and using rational structure-based and physics-informed approaches to support therapeutic discovery.
Summary Generated by Built In
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 OverviewRepertoire 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
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 OverviewRepertoire 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.
- 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.
Recruitment & Staffing Agencies: Repertoire Immune Medicines (“Repertoire”) does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Repertoire or its employees is strictly prohibited unless contacted directly by Repertoire’s internal Human Resources team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Repertoire, and Repertoire will not owe any referral or other fees with respect thereto.
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.
Repertoire is proud to be an Equal Opportunity Employer.
Recruitment & Staffing Agencies: Repertoire Immune Medicines (“Repertoire”) does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Repertoire or its employees is strictly prohibited unless contacted directly by Repertoire’s internal Human Resources team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Repertoire, and Repertoire will not owe any referral or other fees with respect thereto.
Skills Required
- PhD in computer science, computational biology, or a related quantitative field
- 2-5 years of industry experience in protein engineering and design
- Hands-on experience training and fine-tuning protein language models and structure-prediction models
- Experience developing applied AI pipelines for biological data
- Ability to reason about protein-protein interactions using rational structure-based approaches
- Experience using physics-based methods and machine learning workflows
- Strong programming skills in Python
- Experience with multi-GPU training using PyTorch and related libraries
- Experience analyzing and modeling complex, high-dimensional biological datasets using sound computational and statistical practices
- Experience working with TCR-pMHC binding
- Intellectual curiosity, scientific rigor, and enthusiasm for a fast-paced research environment
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The Company
What We Do
Repertoire Immune Medicines is a biotechnology company dedicated to creating treatments for diseases based on the power of the human T cell repertoire to eliminate cancer cells, target pathogens, and regulate immune function in autoimmune disease. The company’s proprietary DECODE™ platform provides a comprehensive understanding of the interactions between T cell receptors and their antigens in disease. DECODE uniquely elucidates the entire immune synapse, including the T-cell receptor-epitope pairs that defines it, the HLA context, and the T cell phenotype. This capability enables the creation of new and potentially transformative classes of immune-based medicines. Repertoire believes the ability to decipher these interactions represents one of the greatest opportunities for innovation in medical science. The company is utilizing the discoveries from DECODE to design and develop novel immune therapies for multiple therapeutic areas, such as autoimmune diseases, infectious diseases, and cancer. The team operates from sites in Cambridge, Massachusetts and Zurich. To learn more about Repertoire, please visit www.repertoire.com.
