Scientist / Senior Scientist, Library Prep

What we are looking for in you

Glyphic is seeking a Scientist or Senior Scientist to lead research on the library preparation stage of our single-molecule protein sequencing platform. Reporting to the Director of Assay Development, you will own how DNA molecules produced by our protein sequencing assay (ProSE) are prepared for and read on the nanopore, the last steps of the assay through library prep to sequencing. ProSE outputs are not standard sequencing templates and they impose constraints that off-the-shelf kits don’t address. As a successful scientist in this role, you will design creatively around those constraints and turn one-off gains in accuracy and read count into results the team can reproduce run after run.

The ideal candidate thinks about the whole system: how upstream chemistry, construct design, and what happens on a nanopore flow cell each shape the data. You have developed library prep methods for demanding templates and are comfortable working independently on open-ended problems. Direct nanopore experience is welcome but not required. We care more that you can learn a new platform quickly and reason from first principles about what you’re seeing. 

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

What you’ll do

Library preparation and method development:

• Own library prep method development for nanopore sequencing end to end: multiplexing, sample barcoding, second-strand synthesis, end repair, and adapter ligation. The goals are to maximize read count and efficiency and reduce run-to-run variability.
• Own the steps at the interface between our protein sequencing assay and library prep. Design and test new approaches to make accuracy gains reproducible.
• Develop on-bead preparation and clean-up methods for high-sensitivity sequencing from low-input material, along with characterization assays that track efficiency, yield, purity, and construct integrity at each stage.
• Feed library prep requirements back into the design of upstream constructs and oligos, working with the scientists who design them.
• Contribute to experimental design for ProSE studies and sequencing runs, and work with automation to move proven manual workflows onto automated platforms.

Mechanistic investigation and troubleshooting:

• Investigate and resolve yield-limiting artifacts from protein sequencing assay chemistry, and DNA library characteristics that reduce yield or bias results. This includes modified nucleotides and secondary structure during second-strand synthesis and end repair. Use computational tools (SnapGene, mFold, NUPACK) and validate predictions at the bench.
• Use sequencing data as a measurement of the whole system. Work with bioinformatics to correlate library preparation variables with read counts, pore health, and classification accuracy, and design experiments that explain what you see.

Leadership and collaboration:

• Provide technical guidance and research experiment design to team members running routine library prep.
• Work closely with oligo synthesis, assay development, integration, automation, and bioinformatics teams to optimize the full sample-to-sequencer pipeline, and maintain rigorous documentation.

What you need

Required:

• PhD in Molecular Biology, Biochemistry, Bioengineering, Chemical Biology, or a related field, with 1+ years of industry experience. Alternatively, an MS with 5+ years of relevant experience.
• Demonstrated experience developing or substantially re-engineering a sequencing library prep method for demanding templates, beyond running existing kits. Examples include low-input, PCR-free, single-molecule, single-stranded, or damaged DNA.
• Deep understanding of enzymatic DNA manipulation (ligation, end repair, phosphorylation, polymerase extension, and adapter attachment), including how the enzymes involved actually work.
• Experience working with chemically modified DNA or RNA, and troubleshooting nucleic acid secondary structure and its effect on reaction or sequencing performance.
• End-to-end systems thinking: the ability to reason about how upstream chemistry, construct design, and sequencing hardware each contribute to a result, and to design experiments that separate them.
• Demonstrated ability to reason from first principles to predict reagent and condition efficacy, rather than relying solely on empirical screening.
• Proficiency with DNA characterization and QC methods such as capillary or gel electrophoresis.
• Experience guiding the bench work of others, such as research associates, students, or junior scientists.
• Excellent problem-solving skills and strong attention to detail
• Excellent written and verbal communication skills, with the ability to collaborate effectively across diverse scientific and technical backgrounds.
• Ability to thrive in a fast-paced environment with evolving priorities.

Nice to have:

• Hands-on experience with nanopore sequencing or another single-molecule DNA sequencing technology such as PacBio.
• Experience characterizing the electrochemical properties of nanopores or related systems (e.g., ion channels, nanoelectrodes).
• Experience with single-stranded DNA or RNA library prep, or PCR-free preparation with modified oligonucleotides in enzymatic workflows.
• Familiarity with automated liquid handling platforms (such as Hamilton, KingFisher).
• Background in protein sequencing, proteomics sample preparation, or peptide chemistry, including oligo-peptide conjugate characterization (LCMS, HPLC).
• 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; and bold, innovative thinking is encouraged
• Direct impact on product development and company direction
• Access to cutting-edge technology in a top tier life science facility
• Ownership of a high-leverage problem at the junction of protein chemistry and DNA sequencing

Professional growth:

• Play a key role in producing patents and publications with significant impact on the field of biological research
• Opportunities for advancement and expanding responsibilities as the organization scales
• Technical leadership experience from day one, guiding a research associate’s work

Compensation
Estimated Base Salary $111,725 - $ 161,950  

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.