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Scientist/Sr. Scientist, Molecular Biology Assay Development, Analytical Dev.

Encoded Therapeutics Inc.
California, Kentucky, US
Closing date
Dec 9, 2022

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Encoded Therapeutics Inc. is a biotechnology company advancing precision medicines for a broad range of genetic disorders. Our mission is to unlock new opportunities for viral gene therapy through genomics-driven discovery. We focus on delivering life-changing advances for individuals with genetic disorders not addressable with current approaches. For more information, please visit

Position details

This is a unique opportunity to work at the intersection of genomics and therapeutics and participate in the development of a diverse therapeutic pipeline driven by a transformative core technology. The position is part of the Analytical Development team at South San Francisco and will work on molecular biology assay development and characterization of AAV-based gene therapy products.

As a Scientist/Sr. Scientist in Molecular Biology Assay Development, you will contribute to the program's technical base by creating and optimizing new next-generation sequencing (NGS) assays and workflows for DNA/RNA, or to the program's scientific base by elevating our understanding of the biology of AAV. In this role, you will lead projects to evaluate emergent technologies that have the potential to improve our long-read NGS assays, collect and analyze NGS datasets. You will also work closely with computational biologists to provide biological and technical insights.

The position requires intensive hands-on work and effective collaboration with internal (Technology, Process Development, Preclinical, Bioinformatics) and external parties.

Workplace Mode l: Onsite


* Apply fundamental understanding of molecular biology, nucleic-acid biochemistry, and NGS to develop new molecular assays that span both genome-wide and targeted strategies.
* Stay at the cutting edge of NGS methodology to identify and evaluate new technologies.
* Refine and optimize existing NGS assays by characterizing assay performance and implementing workflow and protocol improvements (including nucleic acid extraction, library preparation, and other wet-lab methods).
* Collaborate with computational biologists (internal and external) to build analysis pipelines that appropriately integrate new molecular technologies.
* Analyze experiment data, organize results, verifies data integrity, performs statistical analysis, and visualizes data using appropriate software.
* Maintain accurate and well-organized laboratory records, including worksheets, lab notebooks, inventories, and databases.
* Author and review study plans, technical development reports, and SOPs.
* Trains and supervises Research Associates, interns, contractors, and other laboratory personnel


* PhD (or equivalent industry experience) in molecular biology, biochemistry, genetics, cancer biology, immunology, or a related field.
* 4+ years post-PhD experience in NGS assays.
* Proven track record of developing new methods for NGS-based protocols that go beyond commercially available kits.
* Ability to perform NGS data analysis to enable experimental iteration independent of external support.
* Experience managing, mentoring, and training junior scientists or research associates.
* Experience in authoring and reviewing SOPs, developmental and technical reports.
* Personnel characteristics of integrity, teamwork, and commitment to excellence to fit with Encoded core values for success.

Preferred Qualifications

* Knowledge and Experience with AAV
* Experience with long-read sequencing assays (e.g., Pac bio, Nanopore)
* Experience with qPCR/ddPCR assays
* Experience with gene therapy and/or drug development


* 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 kitchen
* Purple Tie dry cleaning service
* Fitness center

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.

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