Staff / Senior Scientist, Assay Development (Library Prep)

Glyphic Biotechnologies • Berkeley, CA

1d • Onsite

About The Position

At Glyphic Biotechnologies, we plan to create the protein revolution for which scientists and researchers have been waiting. We are developing a massively parallel, single-molecule proteome sequencing platform that will transform life science discovery and usher in a new era of insights into human biology and disease. To date, we have raised >$80M from venture partners and non-dilutive grant funding to achieve our vision of next generation proteome sequencing.
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 own the design, optimization, and troubleshooting of complex library preparation workflows for nanopore sequencing.
The ideal candidate thrives at the bench in a dynamic research environment, bringing a mechanistic understanding of enzymes and the creativity to solve complex technical challenges. You iterate quickly on experimental designs, communicate effectively across multidisciplinary teams, and are energized by intellectually stimulating, highly collaborative work.
This role will have the unique opportunity to directly shape the future of single-molecule protein sequencing, enabling transformative discoveries in life science by making robust, scalable, and real-world-ready sequencing solutions a reality.
This is a full-time, exempt, in-person position with work conducted at our Berkeley, CA location.

Requirements

• An advanced degree in Molecular Biology, Biochemistry, Bioengineering, Chemical Biology, or a related field, and relevant industry experience: MS/PhD with 8+/6+ years of experience (for Staff Scientist) MS/PhD with 6+/4+ years of experience (for Senior Scientist)
• Deep understanding of enzymatic DNA manipulation: ligation, end repair, phosphorylation, polymerase extension, and adapter attachment.
• Experience working with chemically modified DNA or RNA and troubleshooting nucleic acid secondary structures and their effect on reaction or sequencing performance.
• Hands-on experience designing, optimizing, and troubleshooting library preparation workflows (manual and automated) for next-generation sequencing.
• Deep expertise in molecular biology and DNA characterization techniques.
• Experience prepping libraries with low input and DNA damage.
• Proficiency with capillary electrophoresis or gel-based QC methods for assessing library quality.
• Demonstrated ability to reason from first principles to predict reagent and condition efficacy, rather than relying solely on empirical testing

Nice To Haves

• Direct experience with Oxford Nanopore library preparation kits.
• Experience working with single stranded DNA or RNA library prep, PCR-free preparation of DNA with modified oligonucleotides in enzymatic workflows.
• Familiarity with automated liquid handling platforms (Hamilton, KingFisher) for library preparation.
• Experience with oligo-peptide or oligo-protein conjugate preparation and characterization (LCMS, HPLC).
• Background in protein sequencing, proteomics sample preparation, or peptide chemistry.
• Comfort using AI tools (Claude, Claude Code) to accelerate literature review, protocol design, and data analysis.

Responsibilities

• Own the end-to-end library preparation workflow to prepare DNA molecules for nanopore sequencing, including strategies for multiplexing, sample barcoding, second strand synthesis, end repair, and adapter ligation.
• Develop efficient methods for on-bead preparation and clean up to enable high sensitivity sequencing from low input material
• Develop characterization assays to monitor efficiency, yield, purity, and construct integrity of products generated at each stage of library preparation
• Contribute to experimental design for ProSE studies and multi-cycle sequencing runs.
• Translate manual to automated workflows
• Investigate and resolve yield-limiting artifacts arising from protein sequencing assay chemistry.
• Diagnose and mitigate DNA library characteristics that reduce yield or bias sequencing results.
• Evaluate modified nucleotides and alternative enzymatic strategies to suppress problematic secondary structures during second-strand synthesis and end repair.
• Analyze constructs for structural issues using computational tools (SnapGene, mFold, NUPACK) and validate predictions experimentally.
• Work with bioinformatics to correlate library preparation variables with sequencing outcomes (read counts, pore health, classification accuracy).
• Partner with bioinformatics to understand how library preparation choices (barcoding strategy, tailing, secondary structure) affect downstream classification accuracy and signal quality.
• Work closely with oligo synthesis (modified DNA design and purity), assay development (protein sequencing workflow), automation (KingFisher and Hamilton workflows), and Bioinformatics to optimize the full sample-to-sequencer pipeline.
• Maintain rigorous experimental documentation in Confluence and Google Sheets; contribute to standardized reporting for each sequencing run.

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: Mid Level
• Number of Employees: 1-10 employees