Senior Bioinformatics Engineer, Infrastructure

Repertoire Immune Medicines, Inc.; Watertown (MA); On-site; USD 160,000 - 185,000; Full time

Job summary

Repertoire Immune Medicines is seeking a Senior Bioinformatics Engineer to join our Computational Engineering team to power discovery of immune medicines from our data-rich datasets. You will build end-to-end pipelines, data platforms, and scalable systems across target discovery, screening, pre-clinical development, and clinical analyses.

Ideal candidates bring 5+ years in biology-data systems, strong containerization and cloud infra skills, and a collaborative mindset to work with ML/Comp Bio

Qualifications

• Bachelor’s or Master’s degree in computer science or related coding-heavy field.
• 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).
• 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.

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.

Education

Bachelor’s or Master’s degree in computer science, software engineering, bioinformatics, or related coding-heavy majors

Tools

Docker

AWS CDK

AWS Step Functions

S3

EC2

Job description

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 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.

Repertoire is committed to building an inclusive culture. Much as the power of the immune system lies in the diversity of T and B cells, we believe our best work comes from a diverse workforce—and we are committed to pursuing that in all facets of the work experience.

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.