Staff / Senior Scientist, Assay Development (Library Prep)

About Glyphic: 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. 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 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. What you’ll do Library preparation and assay development: 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 Mechanistic investigation and troubleshooting: 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. Cross-functional collaboration and documentation: 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. What you need Required: 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 have: 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. 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. Benefits and Perks: 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 We are an Equal Opportunity Employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. Individuals seeking employment at Glyphic Biotechnologies are considered without regard to race, color, religion, national origin, age, sex, marital status, ancestry, physical or mental disability, veteran status, gender identity, or sexual orientation.