Metagenomics Scientist

Applications closed on 2026-02-08

  • Project/division: Nucleic Acid Observatory
  • Start date: as soon as possible
  • Status: full-time SecureBio employee
  • Starting compensation: $130,000 to $150,000, depending on experience
  • Visa sponsorship available: No
  • Work location: In-person in Cambridge, MA

The role

The Nucleic Acid Observatory is building a metagenomics-based pathogen-agnostic early warning system to protect the world from catastrophic pandemics. As advances in biotechnology lower the barriers to engineering pathogens, our mission is to ensure humanity’s detection and alert systems are ready. As part of this mission, we operate a pilot biosurveillance network that performs weekly metagenomic sequencing of wastewater and nasal swabs to screen for engineered threats.

We’re looking for a Metagenomics Scientist to design, develop, and operate innovative metagenomic laboratory methods for detecting both known and novel pathogens from complex samples. A high-performing hire will take ownership of our high-throughput sequencing pipeline, mentor junior scientists, and collaborate closely with our computational team to build an end-to-end biosurveillance system.

Responsibilities

  • Design and improve metagenomic methods for detecting stealth pathogens from complex environmental and clinical samples
  • Manage and scale a high-throughput metagenomics pipeline, ensuring quality and consistency across sample processing
  • Mentor junior scientists on sequencing library optimization for Illumina and Oxford Nanopore platforms
  • Develop automated workflows for nucleic acid extraction and library preparation
  • Collaborate with computational biologists on end-to-end pipeline design and improvement
  • Monitor quality control metrics and diagnose system failures systematically
  • Conduct proof-of-concept experiments and drive pilot studies transitioning concepts to production workflows
  • Maintain documentation, data versioning, and scientific rigor
  • Report pipeline performance and development progress to leadership

Competencies and qualifications

Required

  • PhD with 2+ years of applied experience, or MS with 5+ years of experience, in microbiology, molecular biology, genomics, or a related field
  • Deep hands-on metagenomic workflow experience including library preparation and sequencing at scale
  • Proficiency with metagenomic data analysis and experience collaborating with computational teams
  • Strong experimental design and scientific communication skills

Preferred

  • Experience developing and validating novel NGS assays for pathogen detection
  • Background integrating automated extraction and library preparation platforms
  • Knowledge of enrichment, depletion, or bias-mitigation strategies in metagenomics
  • Publications or patents in relevant areas

Salary and benefits

This is a full-time, in-person role in our Cambridge, Massachusetts office. 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

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

Flexible work schedule

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

Development opportunities

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

401(k)

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

Application process

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 screening interview. High-performing candidates may be invited to further interviews, followed by an in-person work trial in our Cambridge, MA office. We will also require two to three reference checks.

We’re committed to fostering a culture of inclusion, and we encourage individuals with diverse backgrounds and experiences to apply. We especially encourage applications from women, gender minorities, and people of color who are excited about contributing to our mission, and are happy to consider applicants from overseas. We’re an equal opportunity employer.

If you need assistance or an accommodation due to a disability, or have any other questions about applying, please contact .

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Referral bonus

We offer a referral bonus of up to $4,500 to individuals who refer successful candidates for this position:

To receive these bonuses, we must reasonably believe that you were responsible for referring the candidate to us (e.g. due to you introducing them to us when we didn’t previously know them, or them mentioning you on their application as the reason they heard about the position).

  • If you refer a candidate that we invite to a technical interview, you will receive $100;
  • If you refer a candidate that we invite to an in-person work trial, you will receive a further $500, for a total of $600;
  • If the candidate accepts a job offer from us, you will receive a further $1,700, for a total of $2,300;
  • If the candidate is still working with us after three months, you will receive a further $2,200, for a total of $4,500.