Engineer III, Site Engineering & Facilities

Encoded Therapeutics is a clinical-stage biotechnology company developing precision genetic medicines to transform the lives of patients with severe neurological disorders. The company’s vector engineering platform enables potent and cell-type-selective regulation of gene expression, allowing for targeted modulation of disease-relevant genes. Encoded is advancing a pipeline of programs across genetic epilepsies and other neurological disorders with significant unmet need. With integrated discovery, development, and manufacturing capabilities, Encoded is positioned to efficiently move programs from concept through the clinic. Encoded is driven by a mission to meaningfully improve the lives of patients and families affected by devastating neurological disorders. For more information, please visit www.encoded.com.

As an Engineer III, Site Engineering & Facilities, you will be a key technical driver in the design, implementation, and lifecycle management of single-use manufacturing systems within our gene therapy production facility. This role serves as a vital cross-functional partner to Manufacturing, Process Sciences, Supply Chain, and Quality Assurance, ensuring that our viral vector production remains compliant, efficient, and innovative within a cGMP environment.

Core Responsibilities:
Engineering Standards & Automation

• Standard Development: Serve as a core member of the FUME team, contributing to the creation and application of site-wide engineering and automation standards.
• Capital Support: Provide technical support for site engineering and facility capital projects. Take ownership of small-scale projects, managing design, procurement, and implementation.

Equipment Lifecycle Management

• Technical Execution: Execute the full lifecycle of automation and equipment for internal groups, including specification, procurement, testing, onboarding, and qualification (IQ/OQ/PQ).
• Validation & Maintenance: Sustain the validated state of site equipment through robust preventative maintenance and calibration systems.
• Vendor Management: Manage vendor service and calibration contracts, review turnover packages, and coordinate on-site service schedules.

Manufacturing Operations & Compliance

• Manufacturing Support: Deliver real-time troubleshooting for active manufacturing campaigns. Coordinate repairs with external vendors to minimize downtime (includes on-call/weekend support as needed).
• Quality Documentation: Partner with QA to lead the lifecycle management of engineering documentation, including SOPs, Change Controls, and GEP (Good Engineering Practice) protocols.
• EHS & Regulatory: Maintain 100% compliance with internal EHS guidelines, site registrations, and cGMP/environmental regulations.

Training & Mentorship

• Skill Development: Act as a subject matter expert (SME) by providing technical training on new equipment and operational procedures to the wider site team.

Requirements

• Education: Bachelor’s degree in Engineering (Mechanical, Chemical, or Bioengineering preferred).
• Experience: 5-9 years of directly relevant experience in the biotech, pharmaceutical, or gene therapy space.
• Technical Knowledge: Proven expertise in facility, process, or manufacturing engineering. Single-use technology and viral vector manufacturing experience is highly preferred.
• Regulatory Fluency: Deep understanding of cGMP systems and FDA/EU regulations.
• Operational Flexibility: Ability to provide on-call or in-person support for batch processing operations.
• Soft Skills: Strong troubleshooting, organizational, and interpersonal skills. Must be a proactive team player.
• Travel: Ability to travel up to 10% for vendor visits or headquarters requirements.

Benefits

• Health Care Plan (Medical, Dental & Vision)
• Retirement Plan (401k)
• Life Insurance (Basic, Voluntary & AD&D)
• Paid Time Off (Vacation, Sick & Public Holidays)
• Family Leave: (Maternity, Paternity)
• Short Term & Long Term Disability
• Training & Development
• Stocked micro-kitchen with drinks and snacks
• Wellness Resources

Employees (and their families) may obtain medical, dental, vision and basic life insurance benefits through the company and enroll in our company’s 401k plan. Employees will also accrue vacation time off and paid sick time off and may become eligible for paid parental leave. Employees will also enjoy designated paid holidays throughout the calendar year.

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.