Deep Learning Scientist II, Protein Sciences
Repertoire Immune Medicines · Watertown, MA ·
- Category
- ML ai
- Experience
- 2+ years
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.
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.