Systems Integration Engineer

Pilgrim; San Francisco (CA); On-site; USD 135,000 - 175,000; Full time

Job summary

Pilgrim is building America’s biology prime — engineering, manufacturing, and deploying advanced biotechnology for defense and national security. Our ARGUS platform automates biological workflows and requires robust integration across biology, fluidics, and controls.

As a Systems Integration Engineer/Scientist, you will adapt sample prep, qPCR, and sequencing workflows to ARGUS, design tests, troubleshoot failures, and translate scientific advances into reliable, field-ready systems.

Qualifications

• Strong foundation in bioengineering, molecular biology, biochemistry, or related field.

Responsibilities

• Adapt sample preparation, reagent handling, qPCR, and sequencing methods to automated workflows on ARGUS.
• Define operating requirements for workflows, including sample and reagent volumes, timing, temperature, and contamination control.
• Establish bench baselines and compare automated performance using recovery, inhibition, sequencing quality, and processing time.
• Design and run integration tests from individual fluidic and instrument subsystems through complete sample-to-result workflows.
• Isolate failures across biology, fluidics, sensing, controls, and instrument software; verify causes and fixes experimentally.
• Test workflow repeatability across operating conditions and verify performance after changes to hardware, software, reagents, or protocols.
• Maintain test plans, run records, protocol versions, and instrument configurations so failures can be reproduced and fixes tracked.

Skills

Bioengineering

Molecular biology

Biochemistry

Laboratory automation

Troubleshooting

Education

MS or PhD preferred

Tools

Liquid handlers

Microfluidics

Cartridge-based systems

Custom hardware

Scientific instrument development

Job description

Pilgrim is building America’s biology prime - engineering, manufacturing, and deploying advanced biotechnology for defense and national security. Our primary platform, ARGUS, is a fully autonomous system for detecting biological threats in near real time, from naturally occurring pathogens to engineered agents.

We engineer hardware for biology, turning breakthrough science into fielded capabilities. Based in Redwood City, our team brings together mechanical and electrical engineering, chemistry, and biology under one roof to deliver critical technologies to the people who need them.

Pilgrim has raised over $30 million to date and is backed by Peter Thiel, Brian Armstrong, Fred Ehrsam, Dylan Field, and Bryan Johnson, alongside Buckley Ventures, Conviction, Cantos, and others.

About the Role:

As a Systems Integration Engineer/Scientist at Pilgrim, you’ll turn biological methods into automated workflows on ARGUS. You’ll adapt sample preparation, reagent handling, qPCR, and sequencing preparation to the system, troubleshooting failures across biology, fluidics, and controls. Working with scientists and engineers, you will translate scientific advances into integrated systems that perform reliably in the real world.

Responsibilities:

• Adapt sample preparation, reagent handling, qPCR, and sequencing preparation methods to automated workflows on ARGUS.
• Define operating requirements for those workflows, including sample and reagent volumes, timing, temperature, and contamination control.
• Establish bench baselines and compare automated performance using recovery, inhibition, sequencing quality, and processing time.
• Design and run integration tests from individual fluidic and instrument subsystems through complete sample-to-result workflows.
• Isolate failures across biology, fluidics, sensing, controls, and instrument software; verify causes and fixes experimentally.
• Test workflow repeatability across operating conditions and verify performance after changes to hardware, software, reagents, or protocols.
• Maintain test plans, run records, protocol versions, and instrument configurations so failures can be reproduced and fixes tracked.

Qualifications:

• Strong foundation in bioengineering, molecular biology, biochemistry, or a related field. MS or PhD is a plus, not required.
• Experience adapting laboratory protocols to automated instruments, liquid handlers, or custom hardware.
• Ability to troubleshoot biological workflows and instrumentation using assay results, sensor readings, instrument logs, and bench measurements.
• Experience designing comparisons between bench and instrument performance, selecting controls, and setting measurable acceptance criteria.

Preferred:

• Experience with laboratory automation, liquid handling, microfluidics, cartridge-based systems, or development and testing of scientific instruments.

Pilgrim is an equal opportunity employer. We do not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, veteran status, or any other characteristic protected by law. Certain positions require access to export-controlled information and are limited to U.S. Persons as defined by applicable export control regulations.