Metagenomics Scientist

• Starting compensation: $130,000 to $150,000, depending on experience
• Work location: In-person in Boston, MA
• Final date to receive applications: Sunday, February 8th

Secure Bio is building a pathogen-agnostic early warning system to protect the world from catastrophic pandemics. As advances in biotechnology reduce the barriers to engineering pathogens, our mission is to ensure detection and alert systems are ready. We develop methods to identify known and novel biological threats early, including those spreading without obvious symptoms.

The Metagenomics Scientist role centers on the design, development, and operation of innovative metagenomic laboratory methods that can reliably process a continuous stream of diverse samples, from extraction through sequencing and analysis in collaboration with the computational team. The focus is on sensitive detection of stealth pathogens, both known and unknown, from RNA and DNA in complex samples.

The Metagenomics Scientist is expected to work both independently and collaboratively with a strong sense of scientific creativity and operational scalability, ensuring that the best methods are selected or developed so that the pipeline is cutting edge, robust, repeatable, and fast enough to support real-world biosurveillance.

Design, invent, and improve metagenomic laboratory methods for sensitive and unbiased detection of stealth pathogens. This includes executing experiments and troubleshooting to solve challenging detection problems.

Own and evolve a high-throughput metagenomics pipeline, ensuring samples can be rapidly processed, sequenced, and analyzed with consistent quality.

Mentor junior scientists and research associates on a variety of tasks, including optimization of sequencing libraries for Illumina and Oxford Nanopore platforms.

Design and improve automated workflows for nucleic acid extraction and library preparation, adapting protocols for scale and reliability.

Partner closely with the computational biology team to co-design scalable end-to-end pipelines and iteratively improve performance based on downstream results.

Monitor pipeline health using QC metrics and analytical outputs; diagnose failure modes and implement systematic fixes rather than one-off workarounds.

Drive pilot studies and proof-of-concept experiments that transition promising ideas into production-ready workflows.

Maintain rigorous documentation, versioning, and data provenance while operating in a fast-moving, production-adjacent environment.

Report about pipeline performance, risks, and opportunities to cross-functional stakeholders and leadership.

PhD with 2+ years of applied experience or MS with 5+ years of applied experience in microbiology, molecular biology, genomics, microbial ecology, or a related field.

Deep hands-on experience with molecular metagenomic workflows, including preparing libraries and operating Illumina and/or Oxford Nanopore sequencing platforms at scale.

Working proficiency with metagenomic data analysis and strong ability to collaborate with computational biologists from end-to-end across a pipeline.

Strong experimental design skills, scientific communication skills, and enthusiasm for collaborative, interdisciplinary work.

Experience developing or validating novel NGS assays for pathogen detection or discovery.

Experience integrating automated extraction and library preparation platforms.

Familiarity with enrichment, depletion, or bias-mitigation strategies for metagenomics.

Track record of scientific output such as publications and patents.

This is a full-time, in-person role, reporting to the Nucleic Acid Observatory's Head of Laboratory Science in our Boston, Massachusetts lab space. The starting salary range is $130,000 to $150,000 per annum, depending on prior experience. There may be flexibility in salary for exceptional candidates with significant relevant experience.

Our employee benefits reflect our belief in investing to build the strongest possible team, in which everyone receives the trust and support they need to excel. Our benefits package includes:

Comprehensive healthcare coverage, including health, dental & vision insurance, as well as a yearly mental health allowance for every employee.

Flexible work hours; unlimited paid time off (PTO) for all employees; and minimum 12 weeks fully-paid parental leave.

Generous professional development opportunities, including fully-paid conference sponsor ships and a yearly development allowance for every employee.

Employer 401(k) match up to 4% of total salary.

We will review applications on a rolling basis, and are looking for someone to start as soon as possible.

After considering your written application, we may invite you to a short initial work test or screening interview. High-performing candidates may be invited to further interviews, followed by an in-person work trial. We will also require two to three reference…