Principal Scientist Assay Development Jobs (NOW HIRING)

What we are looking for in you

We are seeking an experienced, hands-on Assay Development Scientist to design and perform experiments that enable the next generation of sensitive, accurate, and scalable single-molecule protein sequencing. Reporting to the Director of Assay Development, you will leverage your molecular biology and nucleic acid biochemistry expertise to design, optimize and troubleshoot complex peptide and DNA preparation workflows for nanopore sequencing.

A core dimension of this role is translating manual bench workflows into robust and scalable automated protocols. You will be the primary liaison between assay development and automation engineering - defining workflow parameters, specifying liquid-handling requirements, and executing biological verification studies on multi-instrument automated systems. You will set the requirements, validate the outcomes, and own the scientific documentation.

This is a full-time, exempt, in-person position with work conducted at our Berkeley, CA location.

What you'll do

• Develop, optimize, and transfer complex assay workflows onto automated liquid handling systems and integrated work cells - including high-throughput functional, molecular, chemical, and enzymological assays.
• Partner with automation engineers to translate assay requirements into precise workflow parameters, liquid-handling specifications, and biological acceptance criteria; ensure that implemented protocols meet performance specifications.
• Define critical assay conditions and contribute to experimental design for ProSE studies and multi-cycle sequencing runs, serving as the scientific voice in automation development discussions.
• Design and execute experiments that bridge chemistry and molecular biology; develop a mechanistic understanding of how reagents, materials, environmental conditions, and platform choices impact assay outcomes; evaluate assay sensitivity and robustness across varying inputs.
• Bring fit-for-purpose thinking and creative flexibility to protocol development - balancing robustness and reproducibility with the adaptability needed to respond as scientific questions, platform capabilities as project requirements evolve.
• Collaborate with the Automation team to identify and resolve throughput bottlenecks, leveraging workflow design, work cell configuration, and reagent selection to enable scalable end-to-end assay operations.
• Execute process qualification and optimization studies on automated assay platforms; generate and analyze performance data, identify failure modes, and communicate results to cross-functional stakeholders.
• Distinguish biology-driven failures (such as enzyme activity loss, reagent degradation, or template secondary structure effects) from hardware or software issues on automated platforms; communicate root-cause findings to automation engineers and implement corrective actions on the assay side.
• Author and maintain SOPs, technical guides, and verification documentation for both manual and automated peptide and DNA preparation workflows, written to a standard suitable for handoff to automation engineers and for onboarding new team members.

What you need

Required:

• Advanced degree in chemical biology, biochemistry, molecular biology  or a related field
• Industry experience developing and transferring complex, multi-step assay workflows onto automated liquid handling platforms.
• MS/PhD with 6+/4+ years of experience (for Senior Scientist)
• MS/PhD with 8+/6+ years of experience (for Staff Scientist)
• Deep expertise in molecular biology, biochemistry, and protein and nucleic acid characterization techniques.
• Hands-on experience designing, optimizing, and troubleshooting multistep assay workflows across diverse analyte classes, including: nucleic acids, proteins, and small molecules.
• Experience developing assays for integrated work cells or multi-instrument automated systems.
• Experience executing process qualification or optimization studies on automated liquid handling platforms (Hamilton, KingFisher, or equivalent); ability to define assay parameters, generate and analyze performance data, and conduct systematic diagnostics to distinguish reagent and assay failures from hardware or software issues.
• Demonstrated ability to author technical documentation for automated workflows: SOPs, verification reports, parameter specification sheets, and handoff documents suitable for use by the automation engineering team.
• Experience automating library preparation for high sensitivity DNA workflows.
• Experience staging sensitive reagents for automated workflows, including managing thermal conditions, aliquot preparation, and on-deck reagent integrity during extended runs.
• Ability to identify and resolve compatibility issues at the interface of assay and automation, including: workflow design constraints, reagent behavior, and timing or environmental factors that affect automated protocol performance.
• Excellent problem-solving skills and attention to detail.
• Excellent written and verbal communication skills, with the ability to work seamlessly with colleagues from diverse scientific and technical backgrounds.
• Ability to thrive in a fast-paced environment with evolving priorities.

Nice to have:

• Direct experience with nanopore sample preparation methods.
• Experience working with single-stranded DNA or RNA prep, PCR-free preparation of DNA with modified oligonucleotides in enzymatic workflows.
• Experience with oligo-peptide or oligo-protein conjugate preparation and characterization (LCMS, HPLC).
• Background in protein sequencing, proteomics sample preparation, or peptide chemistry.

We're looking for a teammate that:

• Navigates complex team dynamics, partnerships, and challenges with creativity and logic.
• Operates with adaptability, urgency, and flexibility in evolving environments, thriving in ambiguity.
• Drives work forward without needing to be asked, taking responsibility for outcomes rather than tasks.
• Treats obstacles as problems to be creatively solved, not reasons something can't be done.
• Applies sound judgment to the best available information, testing, learning, and iterating.
• Shares early and directly when assumptions change, results are unclear, or timelines are at risk.

What you can expect from this role

Work environment:

• Collaborative culture where your ideas and expertise are valued
• Direct impact on product development and company direction

Professional growth:

• Learn from a diverse team of world-class scientists and engineers
• Contribute to first-of-their kind technologies, high-impact publications, and patents

Compensation

Estimated Base Salary  $123,000 - $187,575

This is the pay range for this position that we reasonably expect to pay. Individual compensation is based on various factors including, experience, education, skillset, and geographic location. This range is for the SF Bay Area, California location and may be adjusted to the labor market in other geographic areas.