Encoded Therapeutics is a clinical-stage biotechnology company developing precision gene therapies for severe genetic disorders. We leverage our proprietary target-driven platform to engineer novel AAV-based therapeutics that are precise, durable, and transformative for patients in need.
Encoded is seeking a Senior Research Associate that will serve to provide Molecular and Quality Control support for early-stage gene therapy candidates. We are seeking a highly motivated and detail-oriented Senior Research Associate to join our team. This dual-focused role spans both Analytical Development within the Molecular Team and hands-on Quality Control testing. You will be responsible for performing high-throughput molecular testing to support AAV vector characterization, as well as conducting rigorous QC release and stability testing for GMP lots.
Perform high-throughput ddPCR and qPCR vector genome bioassays using Bio-Rad QXOne and QX200 systems for AAV product characterization, routinely processing 30 to 60 samples per week to support Research, Process Development, and Manufacturing teams.
Optimize Oxford Nanopore R10 library preparation protocols for AAV samples by refining plasmid DNA isolation parameters, reagent volumes, and incubation conditions to improve workflow consistency, while applying sequencing data to assess vector genome truncation.
Interpret FASTQ and BAM sequencing outputs from R-based pipelines, making parameter adjustments to tailor results to specific experimental contexts.
Conduct in-vitro potency bioassays for AAV product characterization, complementing vector genome quantification by ddPCR.
Execute ddPCR QX-200 bioassays for AAV vector genome titer and residual DNA quantification across GMP lots, strictly adhering to QC/QA documentation standards.
Support drug substance and drug product release and stability testing, including compendial assays for pH, osmolality, and visual appearance.
Author, review, and maintain detailed lab notebooks, standard operating procedures, and analytical report documentation in compliance with company standards, while collaborating closely with cross-functional teams to ensure seamless data handoffs and maintain inventory of critical analytical reagents.
A Bachelor’s degree in Molecular Biology, Biochemistry, Biotechnology, or a related scientific discipline with a minimum of 5 years of relevant hands-on laboratory experience, or a Master’s degree in a related field with at least 3 years of relevant laboratory experience, or equivalent work experience.
Proven hands-on expertise with ddPCR (Bio-Rad QX200/QXOne) and qPCR platforms for vector quantification, along with experience in Oxford Nanopore or Next-Generation Sequencing library prep and basic bioinformatic workflow interpretation such as FASTQ and BAM files.
Practical experience with cell culture, cell-based bioassay, and compendial testing for pH, osmolality, and appearance in a regulated laboratory environment is essential.
Strong organizational skills to manage high-throughput sample workflows under tight timelines, exceptional attention to detail regarding data integrity and QA/QC documentation, and excellent verbal and written communication skills for cross-functional collaboration.
Direct experience in a cGMP-compliant Quality Control testing environment within the gene therapy, biologics, or cell therapy industry.
Familiarity with regulatory frameworks, data integrity principles, and compendial testing requirements (e.g., USP, Ph. Eur.) for release and stability testing.
Practical working knowledge of statistical analysis tools and basic bioinformatic scripting (such as R or Python) to evaluate sequencing data and bioassay metrics.
Direct hands-on experience authoring and revising Quality Control Standard Operating Procedures (SOPs), test methods, and deviation/CAPA technical assessments.
Experience working with Laboratory Information Management Systems (LIMS) or Electronic Lab Notebooks (ELN) for data tracking and inventory management.
Comprehensive benefits package, including competitive employer premium contributions
Meaningful stock option grants
PTO, sick time and holiday pay
Generous Parental Leave program
Pre-tax medical and dependent care programs
STD, LTD, Life and AD&D
Professional development opportunities
Team-building events
Fully stocked micro kitchen
Fitness center at S. San Francisco headquarters
Encoded is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind. Encoded is committed to the principle of equal employment opportunity for all employees and to providing employees with a work environment free of discrimination and harassment. All employment decisions at Encoded are based on business needs, job requirements and individual qualifications, without regard to race, religion or belief, color, national origin, gender, status as a protected veteran, status as an individual with a disability, or any other status protected by the laws or regulations in the location in which we operate. Encoded will not tolerate discrimination or harassment based on any of these characteristics. Encoded encourages applicants of all ages.
If you need assistance or an accommodation due to a disability, you may call us at +1 650-491-0272.
For candidates based in the SF Bay Area, the anticipated salary range for role is 100,000 - 116,000 . The final salary offered to a successful candidate will be dependent on several factors that may include but are not limited to the type and length of experience within the job, type, length of experience within the industry, education, etc. Encoded Therapeutics is a multi-state employer and this salary range may not reflect positions that work in other states.
A hired applicant may be eligible for an annual bonus as well as equity under the company’s stock plan.
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Encoded Therapeutics