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Scientist - Molecular Biology, NGS Discovery Platform

Encoded Therapeutics Inc.
San Francisco, California, US
Closing date
Jun 28, 2022

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Academic / Research, Consultancy/Private Sector
Informatics / GIS
Genetics, Biology
Salary Type
Employment Type
Full time
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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

Encoded is seeking a Scientist to provide Technology Team support for our NGS-based discovery platform to find novel regulatory elements which enable the development of cutting edge AAV gene therapies. We are seeking a reliable and collaborative scientist to lead our screening technology production efforts in a dynamic, team-centered environment. In addition to a strong background in NGS and general molecular biology, the ideal candidate will be able to exercise sound scientific judgement to lead and successfully execute on multiple production and occasional development projects related to NGS screening efforts. The successful candidate will be reliable, collaborative, and able to drive these projects independently.

Workplace Model: Hybrid

  • Primary responsibilities are to manage and execute ongoing projects related to an established NGS screening pipeline as well as other technologies that are central to our discovery platform. This includes but is not limited to the following:
  • Molecular cloning and construction of large-scale plasmid libraries (from design to wet lab execution)
  • Preparing NGS libraries from experimental design to library prep, QC, and loading
  • Construct and primer design and optimization
  • Independently leading, executing and troubleshooting screening campaigns either via in-vitro cell-lines or in collaboration with in-vivo teams to discover lead therapeutic candidates
  • Coordinating tasks across multiple projects and/or technologies as well as planning, prioritizing, and managing duties to meet organizational goals
  • Interfacing with CROs, vector production, and vivarium teams to manage in-vivo experiments
  • Interfacing with Bioinformatics to communicate experimental parameters and research goals to inform NGS data analysis
  • Interfacing with Scientists in downstream areas of the research pipeline
  • Maintaining meticulous records of experimental design and execution
  • Delivering project updates and presentations as needed at team meetings
  • Planning and executing additional cross-functional molecular biology tasks as needed, including but not limited to: DNA/RNA extraction, qPCR, ddPCR, reporter-based assays, western blotting, in-vitro assays
  • Complying with all laboratory safety policies and regulations
  • Background in molecular biology, cell biology, biochemistry, molecular neuroscience, or related field with a strong molecular biology background-PhD with 0-3 years industry experience, MS with 4+ years industry experience, or BS/BA with equivalent industry experience.
  • Must have outstanding working theoretical knowledge of Illumina next-generation sequencing technologies and broad understanding of diverse applications
  • Must have ample hands-on experience with a broad array of Illumina NGS library preparation methods and applications
  • Must have a strong molecular biology skillset with a focus on, but not limited to conventional PCR, qPCR, construct design and molecular cloning/DNA assembly techniques
  • Must be able to work independently and effectively to meet objectives under time constraints, and adapt and align to rapidly changing priorities
  • Outstanding attention to detail and ability to reliably execute SOPs
  • Outstanding communication and interpersonal skills to collaborate in a matrixed environment of cross-functional Research Associates and Scientists
  • Excellent critical thinking and troubleshooting abilities
  • Excellent technical competency and attention to detail
  • Excellent organizational and prioritization skills
  • Experience in data analysis using software such as Excel, JMP and/or R
  • Ability and willingness to quickly learn new concepts and techniques to support development of the Encoded NGS screening pipeline
  • Strong writing skills to support maintaining a detailed and organized electronic lab notebook as well as documenting findings and developing SOPs
  • Ability to present findings, data, and status updates clearly and concisely which includes literacy with presentation software such as PowerPoint
  • Familiarity with construct design and related molecular biology software such as SnapGene, ApE or Genious
Preferred Qualifications
  • Strongly prefer candidates with an understanding of standard bioinformatic and computational approaches for NGS
  • Prior experience with AAV, lentivirus, or other viral vectors, familiarity with current approaches in gene therapy
  • Prior experience with large-scale library cloning and/or lentiviral library screening
  • Comfort with mammalian cell culture and maintenance, transient transfection, viral transduction, and in-vitro based assays
  • Prior animal work, understanding of genetics, and standard delivery approaches in rodent models preferred
  • Experience with long-read NGS platforms such as PacBio and Oxford Nanopore
  • Experience with FACS and other flow cytometry methods
  • Literacy in Python or similar coding language
  • Familiarity with electronic lab notebooks and LIMS systems such as Benchling
  • Experience managing Research Associates
  • 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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