Staff Bioinformatics Engineer

Singular Genomics • San Diego, CA

8d • $129 • Hybrid

About The Position

Singular Genomics is inventing at the forefront of genomics, one of the world’s fastest-growing industries. The commercially available G4® Sequencing Platform is a powerful, highly versatile benchtop genomic sequencer designed to produce fast and accurate results. In addition, the company is currently developing the G4X™ Spatial Sequencer, an upgrade to the G4, which will leverage Singular’s proprietary sequencing technology, applying it as an in situ readout for transcriptomics, proteomics and fluorescent H&E in tissue, with spatial context. Singular Genomics’ mission is to empower researchers and clinicians to advance science and medicine. We foster a culture of creativity and technical excellence, both catalysts for innovation. We celebrate diversity, emphasize collaboration and, as we rapidly mature, we are constantly looking at ways we can do better for our people. Our Headquarters are located on the Torrey Pines Mesa, in La Jolla, California at the center of the biotech hub. Our Manufacturing facility is in Sorrento Valley. POSITION SUMMARY: 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, integrate with operational systems including Slack , Jira and HubSpot, and automate 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 at least quarterly.

Requirements

• 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.

Nice To Haves

• 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.

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.

Benefits

• this role is eligible for one of our variable cash programs (bonus or commission) and may receive equity as part of the compensation package.
• 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 [e-mail]

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: No Education Listed