Associate Director/Principal Scientist, Process Development, Cell Culture

Upstream Process Development
South San Francisco, California, United States
Full time

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

We are recruiting a Process Development Associate Director or Principal to assist in building improved process technologies for rAAV expression. This is a rare opportunity to enter an emerging field, in a company committed to developing first-rate platform capabilities. By enhancing our ability to manufacture rAAV vectors, our work will directly contribute to enabling gene therapies in broader and more challenging indications. The successful candidate will work across multiple projects, and should expect a fast-paced, dynamic environment.


  • Lead a team developing bioreactor-based cell culture processes for manufacturing of AAV gene therapy vectors across multiple preclinical programs and disease areas
  • Direct and execute PD experiments in shaken cultures and stirred-tank bioreactors from 2L-250L scale
  • Develop long-term PD platform strategy in collaboration with PD leadership, and Encoded’s CTO
  • Contribute to development of project-specific Control Strategy in support of GMP manufacturing and regulatory filings
  • Investigate new and alternative process technologies
  • Develop improved cell culture media and feed solutions
  • Optimize existing processes for improved consistency, performance, and product quality, including leadership of process characterization projects.
  • Serve as SME for scaleup and process transfer to manufacturing team; including scaledown experiments, authorship, and review of technical documents. May support MSAT investigations and external CMO manufacturing as-needed.
  • Serve as SME for upstream Process Characterization, including CQA risk assessment, DoE designs for optimization and CPP determination
  • Guide a team in planning and preparation for reliable execution of experiments and high-quality documentation
  • Contribute to expanding capabilities of Upstream PD lab, including identifying new equipment, external vendors, and/or improved workflows.
  • Lead certain process research initiatives and other projects, including cross-functional coordination including Downstream PD, Analytical Development, Research groups, and Technology team.


  • PhD related to bioprocessing, biochemical engineering, or gene therapy and 8 or more years of industry experience designing and operating stirred-tank bioreactor experiments for mammalian cell culture OR
  • Master’s degree related to bioprocessing, biochemical engineering, or gene therapy and 10 or more years of industry experience designing and operating stirred-tank bioreactor experiments for mammalian cell culture
  • Ability to conceptualize and design long-term PD initiatives based on strategic objectives. Will guide and execute experiments, interpret data, present results, and mentor team members in these skills.
  • Experience supporting regulatory filings for IND/IMPD or commercialization, including working knowledge of regulatory guidance documents, and prior service on cross-functional CMC teams.
  • Detailed understanding of bioreactor control systems and relevant engineering concepts (PID control, kLa, etc.), and demonstrated ability to apply this knowledge toward process transfer, scaleup/scaledown, or troubleshooting.
  • Mathematical ability to perform engineering-based experiment design and data analysis, including skill with MS Excel, DoE, and/or other related tools.
  • Enthusiasm for collaborative work in a dynamic environment, plus individual accountability in areas of responsibility
  • Strong verbal and written skills are required, as well as effective interpersonal, technical, and troubleshooting skills

Preferred Qualifications:

  • Experience designing perfusion processes and/or development of medium and feed solutions
  • Experience with single-use bioreactors, AAV expression, large-scale transfection, and/or baculovirus TGE
  • Experience serving as PIP or other direct engagement with manufacturing groups
  • Prior exposure to large-scale GMP manufacturing either by direct experience, or from working in a PD or MSAT setting
  • Knowledge of DoE and JMP or DesignExpert
  • Experience with relevant database and visualization tools
  • Prior engagement in LIMS initiatives, and practical


  • 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

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.