Note: The job is a remote job and is open to candidates in USA. Encoded Therapeutics Inc. is a biotechnology company advancing precision medicines for a broad range of genetic disorders. They are seeking a strategic and execution-oriented Associate Director, Clinical Business Operations to support and optimize the operational infrastructure of their clinical development organization, driving operational excellence and financial oversight.
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
Skills
- 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
- 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
- Experience supporting clinical programs in rare disease, neurology, oncology, cell therapy, gene therapy, or advanced therapeutics strongly preferred
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
- This position may also be eligible for a discretionary annual bonus
- Discretionary stock-based long-term incentives
- Paid time off
- Benefits package
Company Overview
Encoded Therapeutics is creating one-time, disease-modifying gene therapies for pediatric central nervous system (CNS) disorders with its cell-selective targeting and regulation platform. It was founded in 2014, and is headquartered in South San Francisco, California, USA, with a workforce of 51-200 employees. Its website is https://encoded.com/.