Senior Computational Synthetic Biologist

Perimeter; Boston (MA); On-site; USD 120,000 - 180,000; Full time

Job summary

Perimeter is hiring a computational synthetic biologist to advance agnostic detection of genetic engineering in metagenomic NGS data. Building on ENDAR concepts from FELIX, you will help detect engineered biothreats and enable rapid containment.

We seek a PhD (or 5+ years) with 2+ years in genetics/genomics, and strong Python plus NGS analysis experience. Excellent communication and cross-functional teamwork are essential for this role.

Qualifications

• PhD (or five years experience) plus two years experience in genetics, genomics, computational biology, or a related discipline.
• 2+ years of first-hand experience engineering microbes using molecular methods.
• Subject matter expertise in NGS analysis (assembly, alignment, SV calling, annotation).
• Proficiency with Python; ability to work across multiple projects in fast-paced environment.

Responsibilities

• Develop and lead approaches to improve engineering detection capabilities with benchmarking and validation strategies.
• Provide expert assessments of function, purpose and impact when genetic engineering or biothreats are detected.
• Troubleshoot complex problems and propose experimental plans to resolve them.
• Maintain high-quality documentation in reports, notebooks, code comments and software docs.
• Share expertise with the team to raise collective capabilities.

Skills

Genetics

Genomics

Computational biology

Python

NGS analysis

Project management

Communication

Education

PhD or equivalent

Tools

Gibson assembly

Plasmid engineering

Job description

Perimeter is the global biosecurity infrastructure company, purpose-built to protect operational continuity and way of life in an era of accelerating biological threats.

Our end-to-end biosecurity infrastructure platform spans detection, characterization, forecasting, and response — powered by frontier AI and deployed globally across airports, hospitals, wastewater systems, and critical infrastructure. Perimeter enables rapid response —delivering scalable, reliable, software-integrated infrastructure, and converting biointelligence into real-time decisive action for governments and enterprises worldwide.

Additional information about Perimeter's mission, capabilities, and platform is available at https://www.perimeter.bio/

About the Role

We’re hiring a computational synthetic biologist to advance our capabilities for agnostic detection of genetic engineering in metagenomic next-generation sequencing (NGS) data.

Formerly, as a part of Ginkgo Bioworks under IARPA’s Finding Engineering-Linked Indicators (FELIX) program, we developed Engineered Nucleotide Detection and Ranking (ENDAR), the best-in-class set of engineering detection algorithms built under FELIX.

Since then, advances in genetic engineering and the democratization of AI have broadened the landscape for accidental and deliberate creation of engineered biothreats. We seek to detect and contain these before they spread.

If your expertise can assist us in that mission, we’d love to hear from you!

Responsibilities

• Develop and lead technical approaches to improve our engineering detection capabilities, through design of novel approaches or iteration on existing tools. Include benchmarking and validation strategies, milestones, key decision points, and contingency plans.


• When genetic engineering or biothreats are detected, provide expert assessments of function, purpose, and impact, performing follow-up analyses as necessary.


• Independently troubleshoot technically complex problems, and propose solutions or experimental plans to resolve or correct for them.


• Maintain high-quality documentation of your work and discoveries, in the forms of written reports, technical presentations, electronic lab notebooks, internal database records, code comments, and software documentation.


• Share your area of expertise with the team, raising our collective abilities


• PhD (or five years experience) plus two years experience in genetics, genomics, computational biology, or a related discipline. Interdisciplinary work is strongly encouraged.


• 2+ years of first-hand experience engineering one or more microbes, using techniques such as molecular cloning, Gibson assembly, plasmid and chromosomal engineering, conjugation, transformation, or transposon-mediated mutagenesis. Experience engineering multiple organisms is a plus.


• Subject matter expertise in NGS analysis such as assembly, alignment, structural variation calling, and annotation.


• Additional Expertise in one or more of the following areas: bioinformatics, statistics, probabilistic modeling, machine learning, or quantitative modeling of biological systems.


• Proficiency with at least one programming language (Python preferred).


• Demonstrated ability to meet the demands of multiple concurrent projects.


• Ability to work efficiently in a fast-paced, high-growth environment.

Preferred Capabilities & Experience

• Experience in design, development, and validation of novel bioinformatic tools


• Expertise in best practices for software development, including version control, code review, unit testing, containerization, and continuous integration


• Experience using genomic language models or protein language models to characterize or predict features of biological sequences


• Proven track record of delivering in cross-functional teams and in project management


• Excellence in communication to technical, interdisciplinary, and lay audiences


• Experience engineering non-model organisms