Senior Bioinformatics Engineer, Infrastructure

Repertoire Immune Medicines•Watertown, MA

21h•$160,000 - $185,000

About The Position

Repertoire Immune Medicines is seeking a Senior Bioinformatics Engineer to join its Computational Engineering team and help make proprietary immune-synapse datasets discoverable, trustworthy, and ready for internal analysis at scale. The role contributes end-to-end across the protein therapeutic pipeline, from target discovery and screening through preclinical development and clinical trial analyses. It is suited to a self-motivated engineer who builds reliable, correct, maintainable systems. The engineer will build and operate bioinformatics pipelines and durable data platforms, manage secure cloud infrastructure, establish team engineering standards, and own end-to-end data processing and delivery for scientific decision-making. The role also includes developing agentic workflows and harnesses for bioinformatics pipeline development, partnering with machine-learning, computational-biology, and lab-platform users in a fast-paced research environment.

Requirements

Bachelor’s or Master’s degree in computer science, software engineering, bioinformatics, or a related coding-heavy major.
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 desirable. AWS examples include ECS Fargate, EC2, S3, EFS, Step Functions, IAM, VPC, and CDK.
Exposure to workflow/orchestration tools such as Step Functions and Nextflow or Snakemake, and to event-driven patterns.
Ability to partner with ML/Comp Bio and Lab Platform users; clear written and verbal communication with non-engineers; and product/UX instincts for scientific users. Relevant technologies include FastAPI and React/TypeScript.
Intellectual curiosity, scientific rigor, and enthusiasm for 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.
SSO/OAuth integration experience and familiarity with 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, including 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 through clean, well-documented internal APIs, applications, and SQL databases.
Provision and manage cloud infrastructure as code using secure practices that keep systems robust, safe, and maintainable.
Own team engineering standards, including CI/CD test automation, version control, and design and review practices.
Lead incident reviews and preventative improvements, diagnose root causes of failures, and build safeguards 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.