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Role Description

We are hiring a Staff Bioinformatics Platform Engineer to build and own the internal applications and execution platform that run our bioinformatics workflows. You will lead architecture and implementation of tools that support:

• Nextflow pipeline execution on AWS Batch
• Integration with operational systems including Slack, Jira, and HubSpot
• Automation of data flow into our data lake

This is a small-team role combining technical leadership with hands-on delivery. This position can be remote or hybrid/on-site. If remote, travel to the headquarters in San Diego, CA will be required at least quarterly.

Responsibilities

• Own end-to-end Nextflow workflow execution: run launch, configuration, tracking, retries/failures, metadata capture, and auditability on AWS Batch.
• Build internal web apps and services that enable operational workflows (e.g., custom panel design, QC/reporting, run monitoring).
• Integrate pipeline events and outcomes with Slack, Jira, and HubSpot to support scalable operations.
• Lead hands-on data analysis to validate pipeline outputs, investigate anomalies/QC trends, and translate findings into improvements to workflows, tooling, and operational processes.
• Implement automated pipelines for key QC processes (including reagent QC) and land outputs/metadata into Snowflake.
• Define and improve processes around tools: runbooks, quality gates, observability, and operational best practices.

Qualifications

• Senior-level experience building and operating scientific/bioinformatics applications in production.
• Demonstrated experience developing, running, and supporting Nextflow pipelines in production.
• Strong Python engineering skills and experience building backend services/APIs.
• Experience building web applications with React, or equivalent modern front-end framework.
• Experienced in HPC-computing and Linux-based operating systems.
• Experience deploying/operating workflows on AWS, ideally including AWS Batch.
• Experience integrating systems via APIs/webhooks (Slack, Jira, HubSpot or similar).
• Ability to drive architecture decisions, align stakeholders, and implement pragmatic processes in a small team.
• Ability to provide interpretable and actionable results from bioinformatic analyses.

Preferred Qualifications

• Experience in NGS sequencing environments with exposure to single-cell and/or spatial workflows.
• Experience with Snowflake and building automated data pipelines.
• MLOps experience: batch inference/training pipelines, model packaging/registry, monitoring.

Compensation

The estimated base salary range for this role based in the United States of America is: $129,100 - $163,000. Additionally, this role is eligible for one of our variable cash programs (bonus or commission) and may receive equity as part of the compensation package. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Should the level of the role change during the hiring process, the applicable salary range may be updated accordingly.

Equal Opportunity Employer

Singular Genomics is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. Singular Genomics is committed to working with and providing reasonable accommodations to job applicants with physical or mental disabilities. Applicants with a disability who require a reasonable accommodation for any part of the application or hiring process can provide their name and contact information to our Accommodations team at accommodationsrequest@singulargenomics.com. Your request will be responded to as soon as possible.