Staff / Senior Scientist, Assay Development (Automation)

Glyphic Biotechnologies • Berkeley, CA

4d • $123,000 - $187,575 • Onsite

About The Position

Glyphic Biotechnologies is developing a massively parallel, single-molecule proteome sequencing platform. We are seeking an experienced, hands-on Assay Development Scientist to design and perform experiments for sensitive, accurate, and scalable single-molecule protein sequencing. Reporting to the Director of Assay Development, you will use your molecular biology and nucleic acid biochemistry expertise to design, optimize, and troubleshoot complex peptide and DNA preparation workflows for nanopore sequencing. A key aspect of this role is translating manual bench workflows into robust and scalable automated protocols. You will act as the primary liaison between assay development and automation engineering, defining workflow parameters, specifying liquid-handling requirements, and executing biological verification studies on automated systems. You will set requirements, validate outcomes, and own scientific documentation.

Requirements

• 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 Haves

• 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.

Responsibilities

• 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.

Benefits

• Employee Stock Option Plan
• 100% Health Plan Coverage for Employees & Dependents (Medical, Dental, & Vision)
• Employer Retirement Contributions to 401(k)
• Generous Paid Time Off
• Paid Maternity and Paternity Leave
• Health & Wellbeing Program
• Office Snacks and Beverages
• Regular Team Bonding Activities

What This Job Offers

• Job Type: Full-time
• Career Level: Senior