Senior Bioinformatics Engineer, Infrastructure

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 DECODE^TM 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 Watertown, 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 Senior Bioinformatics Engineer to join our Computational Engineering team and help power the discovery of transformational immune medicines from our growing immune synapse database. As one of a small group of high-impact engineers, you will make extensive proprietary datasets discoverable, trustworthy, and ready for internal analysis at scale. This position offers a rare opportunity to contribute end-to-end across the protein therapeutic pipeline, from target discovery & screening through pre-clinical development and clinical trial analyses. This role is ideal for a self-motivated engineer who takes pride in building systems that are correct, reliable, and built to last.

Key Responsibilities

• Build and operate bioinformatics pipelines from instrument to data ecosystem using workflow orchestration and containerized execution.
• Build durable data platforms that support data discovery by exposing data through clean, well-documented internal APIs, applications, and SQL databases.
• Provision and manage cloud infrastructure as code with secure engineering practices that keep systems robust, safe, and maintainable.
• Own engineering standards for the team including CI/CD test automation, version control, and design and review practices that keep systems maintainable as the team grows.
• Lead incident reviews and preventative improvements to diagnose the root cause of failures and build safeguards that prevent recurrence with verifiable gating mechanisms.
• Own end-to-end data processing and delivery to support scientific decision making around the organization.
• Develop agentic workflows and harnesses for developing bioinformatics pipelines.

Qualifications/Experience

• Bachelor’s or Master’s degree in computer science, software engineering, bioinformatics, or related coding-heavy majors, with 5+ years of work experience within the biology domain.
• Proven experience building/operating production data systems or pipelines (bioinformatics, data engineering, platform/SRE, or ML infrastructure; Postgres and S3-backed data storage).
• Hands-on with containers (Docker or Podman) and cloud infrastructure, ideally including infrastructure-as-code (AWS: ECS Fargate, EC2, S3, EFS, Step Functions, IAM, VPC, CDK).
• Exposure to workflow/orchestration (Step Functions and Nextflow/Snakemake) and event‑driven patterns.
• Ability to partner with ML/Comp Bio and Lab Platform users; clear written and verbal communication with non-engineers; product/UX instincts for scientific users (FastAPI, React/Typescript).
• Intellectual curiosity, scientific rigor, and enthusiasm for working in a fast‑paced, evolving research environment.

Preferred Qualifications

• Bioinformatics breadth spanning sequencing, mass spec and imaging, including NGS formats (FASTQ, BAM/CRAM) and specific pipeline experience (Cell Ranger, RNA-seq tooling, HLA typing).
• Familiarity with protein language models, protein structure prediction, and molecular dynamics simulation.
• SSO/OAuth integration; observability tooling (CloudWatch).
• SOC2/ISO27001/GxP exposure.
• Agentic coding fluency – the ability to structure and direct AI coding tools effectively.
• Exposure to enabling ML scientists (artifact stores/registries, dataset versioning).

Compensation and Benefits
The base salary for this role ranges from $160,000 to $185,000 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.