Senior Bioinformatics Engineer, Infrastructure

Repertoire Immune Medicines•Watertown, MA

About The Position

Repertoire Immune Medicines is seeking a Senior Bioinformatics Engineer to join its Computational Engineering team and help make its growing immune synapse database discoverable, trustworthy, and ready for internal analysis at scale. The engineer will contribute across the protein therapeutic pipeline, from target discovery and screening through preclinical development and clinical trial analyses. The role is suited to a self-motivated engineer who values building correct, reliable, and maintainable systems. The position involves building and operating bioinformatics pipelines, creating durable data platforms and secure cloud infrastructure, and establishing engineering standards and practices. The engineer will own end-to-end data processing and delivery to support scientific decision-making and develop agentic workflows and harnesses for bioinformatics pipeline development.

Requirements

Bachelor’s or Master’s degree in computer science, software engineering, bioinformatics, or a related coding-heavy major.
At least 5 years of work experience within the biology domain.
Proven experience building or operating production data systems or pipelines in bioinformatics, data engineering, platform/SRE, or ML infrastructure, including Postgres and S3-backed data storage.
Hands-on experience with containers such as Docker or Podman and cloud infrastructure; infrastructure as code is preferred, with AWS services including ECS Fargate, EC2, S3, EFS, Step Functions, IAM, VPC, and CDK cited.
Exposure to workflow/orchestration tools such as Step Functions and Nextflow or Snakemake, and to event-driven patterns.
Ability to partner with ML/Computational Biology and Lab Platform users.
Clear written and verbal communication with non-engineers, and product/UX instincts for scientific users; FastAPI and React/TypeScript are cited.
Intellectual curiosity, scientific rigor, and enthusiasm for working in a fast-paced, evolving research environment.

Nice To Haves

Bioinformatics breadth spanning sequencing, mass spectrometry, and imaging, including NGS formats such as FASTQ and BAM/CRAM and pipeline experience with Cell Ranger, RNA-seq tooling, or HLA typing.
Familiarity with protein language models, protein structure prediction, and molecular dynamics simulation.
Experience with SSO/OAuth integration and observability tooling such as CloudWatch.
Exposure to SOC2, ISO27001, or GxP.
Agentic coding fluency: ability to structure and direct AI coding tools effectively.
Exposure to enabling ML scientists through artifact stores/registries and dataset versioning.

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 using secure engineering practices to 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 support maintainability as the team grows.
Lead incident reviews and preventative improvements to diagnose root causes 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 across the organization.
Develop agentic workflows and harnesses for developing bioinformatics pipelines.