Associate Director, Development Program Manager

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 www.Encoded.com .

Position Details

Encoded is seeking an Associate Director, Development Program Manager to drive the cross-functional planning and execution of a development program within our AAV gene therapy platform, focused on central nervous system (CNS) indications. Reporting to the Director, Development Program Management, this role is for an experienced program management professional who combines strong organizational and project-management expertise with a solid understanding of the drug development process, ideally including gene therapy or other advanced modalities. The Associate Director will serve as the operational backbone for the program team, working closely with Research, Clinical Development, Regulatory Affairs, CMC, Patient Advocacy and Medical Affairs to ensure program timelines, budgets, risks, and deliverables stay aligned and on track, while partnering with and escalating to the Program Management Organization (PMO) Director on major risks, resourcing conflicts, and strategic trade-offs.

Responsibilities

Program Strategy & Core Team Leadership

Facilitate development and implementation of program strategy, ensuring alignment with company goals, timelines, and budgetary constraints

Organize Development Core Team activities that foster cross-functional collaboration, effective communication, and strategic discussion, ensuring all stakeholders are aligned on program objectives and milestones to aid decision-making

Ensure cross-functional teams are properly prepared for internal meetings, communications to management, and engagement with external partners

Partner with the Director of PMO to ensure portfolio and cross-program considerations alignment

Program Planning & Execution

Develop and maintain the integrated program plan, timeline, and budget across all functional areas (Research, Nonclinical, Clinical, Regulatory, CMC,Medical , Patient Advocacy , Commercial) for the assigned program

Track deliverables resulting from Core Team meetings, ensuring timelines are met and objectives are achieved

Identify program risks and dependencies early, and develop and track mitigation plans in partnership with functional leads, with particular attention to the specialized considerations of AAV gene therapy programs (e.g., viral vector supply timelines, long-term follow-up requirements, specialized dosing or delivery infrastructure for CNS administration)

Assist functional leads with implementing risk management strategies, proactively identifying and mitigating program risks and challenges

Support scenario planning and contingency planning for key program decision points (e.g., go/no-go milestones, regulatory interactions, data readouts)

Contribute to the development and refinement of program management processes, templates, and best practices across the organization

Cross-Functional Coordination

Serve as the primary point of integration across functional areas for the program, ensuring consistent communication of program status, risks, and decisions

Partner with functional leads to coordinate cross-functional projects related to CMC, Regulatory, Clinical, Medical , Patient Advocacy , and Nonclinical, providing support and guidance to achieve project goals

Facilitate internal communication to identify risks and mitigations, escalating unresolved issues to the Director PM as needed

Budget & Resource Management

Partner with Finance and functional leads on budget forecasting

Support resource planning and capacity analysis across functions to ensure the program is appropriately staffed

Communication & Reporting

Monitor and report program progress, providing regular updates to cross-functional teams, the PM Director , and other stakeholders, highlighting key achievements, challenges, and mitigation plans

Utilize formal communication protocols and tools, including dashboards, reports, and weekly/monthly updates, to support company and operational goals

Support maintenance of program documentation in alignment with internal quality and compliance standards

Ad Hoc Projects

Demonstrate flexibility and adaptability to contribute to ad hoc functional projects across various departments

Collaborate with team members to address challenges and find innovative solutions for ad hoc projects, as needed

Support Quarterly Business Review (QBR) and Board of Directors (BoD) meetings as needed

Perform other duties as assigned

Typically requires a minimum of 8 years of related experience with a bachelor’s degree; or 6 years and a master’s degree; or a PhD with 3 years' experience; or equivalent experience.

Advanced degree in life sciences, pharmacology, or a related field preferred; an MBA or project management certification is a plus

Demonstrated experience in program or project management within the biotech, pharmaceutical, or related life sciences industry

Working knowledge of the drug development process, including preclinical, clinical, regulatory, and commercial requirements

Experience supporting gene therapy, AAV vectors, or other advanced modality programs, and/or rare disease programs, strongly preferred

Proven track record of successfully leading and managing cross-functional teams in the development and execution of complex development programs, preferably in gene therapy

Up to 20% travel may be required

Skills and Attributes

Self-starter with the ability to work independently and take initiative

Strong organizational skills with the ability to manage a complex, multi-functional program

Excellent leadership, communication, and interpersonal skills, with the ability to influence and collaborate effectively at all levels of the organization

Strategic thinker with the ability to prioritize and make informed decisions in a fast-paced environment

Strong problem-solving abilities and a proactive, critical-thinking approach to identifying and resolving issues

Willingness to learn and collaborate in a dynamic team environment

Excellent written and oral communication skills, including experience preparing materials for and presenting to senior leadership

Proficient in Smartsheet, Office Timelines and/or other project management tools and software

Proven ability to evaluate existing PMO tooling, workflows, and delivery frameworks; skilled at identifying operational bottlenecks and providing strategic recommendations to modernize and streamline processes.

Comfortable operating in a fast-paced, evolving company environment with the ability to adjust priorities as needed

Preferred Qualifications

PMP certification or equivalent program/project management credential

Experience supporting rare disease or CNS-focused gene therapy programs

Familiarity with gene therapy–specific regulatory considerations

Demonstrated experience leveraging AI-assisted features within modern program and portfolio management tools to automate workflows, synthesize project data, and enhance team productivity.

Experience with governance processes in a biotech or pharmaceutical organization (e.g., portfolio reviews, stage-gate processes)

Familiarity with IND submission

For candidates based in the San Francisco Bay Area the salary range for this position is 170,000 - 205,000

For candidates based outside the San Francisco Bay Area, the salary range is 160,000 - 189,000

Encoded considers a variety of factors when determining base compensation, including experience, qualifications, internal equity and geographic location. Actual compensation will be determined based on relevant skills, experience, qualifications, internal equity, and business needs. This position may also be eligible for a discretionary annual bonus, discretionary stock-based long-term incentives, paid time off, and a benefits package.

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 South San Francisco location

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.