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.

We are seeking a strategic, highly collaborative, and execution-oriented Associate Director, Clinical Business Operations, to support and optimize the operational infrastructure of our clinical development organization. Reporting to the VP of Clinical Operations, this individual will serve as a key business partner across Clinical Operations, Clinical Data Management, and Biometrics to drive operational excellence, financial oversight, and portfolio execution.

The Associate Director will be responsible for the end-to-end lifecycle of vendor outsourcing, from strategic selection through contract execution, active change order management, and financial oversight. This role is ideal for an experienced leader who thrives in a fast-paced environment and enjoys balancing hands-on clinical contracting with long-range financial modeling and planning.

Requirements

Key Responsibilities

• Partner with clinical operations, data management, and biometrics teams to author Request for Proposals (RFPs) and define vendor scopes of work.
• Lead cross-functional bid defense meetings, analyze commercial proposals, perform cost benchmarking, and provide data-driven recommendations to leadership.
• Drive the strategic selection of CROs and specialized clinical vendors, optimizing the vendor portfolio for quality, scalability, and cost-efficiency.
• Partner with Legal and the clinical development team in the drafting, negotiation, and final execution of Master Services Agreements (MSAs), Statements of Work (SOWs), Change Orders and confidentiality agreements across clinical functions.
• Design, author, and standardize SOW templates to streamline vendor onboarding, establish baseline metrics, and reduce execution cycle times.
• Manage the negotiation and execution of Clinical Trial Agreements (CTAs) and investigator budgets for sponsor-managed sites, ensuring rapid study startup.
• Manage an active change order management pipeline to rigorously track contract amendments, budget shifts, and vendor performance.
• Partner closely with study teams to proactively identify operational deviations from the original SOW, mitigating scope creep before it impacts the budget.
• Liaise between Clinical Operations and Corporate Finance to ensure financial alignment across all programs.
• Partner with the Head of Clinical Operations to build robust, multi-year clinical trial budget forecasts, lifecycle cost models, and annual operational plans.
• Support quarterly Budget vs. Actual (BVA) reviews; track investigator grant accruals and vendor pass-through costs, and accurately explain financial variances to leadership.
• Identify operational gaps and implement scalable business processes, tools, templates, and governance mechanisms to improve efficiency, transparency, compliance, and organizational effectiveness.
• Support due diligence, alliance management, and business development activities as needed.
• Champion a culture of accountability, operational rigor, collaboration, and continuous improvement across the Clinical organization.

Requirements

• Bachelor’s degree in life sciences, business, healthcare administration, finance, or related discipline required.
• 7-9+ years of biotechnology, pharmaceutical, or life sciences experience with a heavy emphasis leading clinical outsourcing, clinical finance, or clinical business operations.
• Demonstrated experience in clinical budgeting, forecasting (LRP) and vendor financial management.
• Experience supporting clinical programs in rare disease, neurology, oncology, cell therapy, gene therapy, or advanced therapeutics strongly preferred.
• Strong understanding of clinical development processes, CRO/vendor management models, portfolio planning, and GxP-regulated environments.
• Proven ability to influence across functions and operate effectively with senior leadership in a dynamic, matrixed organization.
• Excellent analytical, financial, organizational, project management, and problem-solving capabilities.
• Exceptional communication and executive presentation skills, with the ability to translate complex operational and financial information into actionable insights.

For candidates based in the SFBA area, the salary range for this position is: $170,000 to $200,000.

For candidates based outside the SFBA area, the salary range is 150,000 to 180,000.

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

Benefits

• 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.