Associate Director, Clinical Business Operations

Encoded Therapeutics Inc.

Associate Director managing clinical business operations at Encoded Therapeutics Inc. Collaborating across teams to drive operational excellence and financial oversight in clinical development.

Posted 6/4/2026full-timeRemote • 🇺🇸 United StatesSenior💰 $150,000 - $200,000 per yearWebsite

About the role

Key responsibilities & impact

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

What you’ll need

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.

Benefits

Comp & perks

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

ATS Keywords

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Applicant Tracking System Keywords

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Hard Skills & Tools

clinical budgetingforecastingvendor financial managementclinical trial agreementsmaster services agreementsstatements of workchange orderscost benchmarkingdata-driven recommendationsoperational deviations

Soft Skills

analytical capabilitiesorganizational skillsproject managementproblem-solvingcommunication skillsexecutive presentation skillsinfluence across functionscollaborationaccountabilitycontinuous improvement