Encoded Therapeutics Inc.

Role Description 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. 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. Qualifications - 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. Requirements - 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.

Role Description We are seeking a highly organized, detail-oriented, and collaborative Clinical Trial Assistant (CTA) to support the execution of clinical studies across our gene therapy development programs. Reporting to the Clinical Operations team, the CTA will provide operational, administrative, and systems support for clinical trials conducted in accordance with ICH-GCP guidelines, company SOPs, and applicable regulatory requirements. This role will partner closely with Clinical Trial/Program Managers, Clinical Operations, Data Management, Regulatory Affairs, Quality, vendors, CROs, and clinical sites to support study execution activities, documentation management, vendor coordination, and inspection-ready clinical operations processes. The ideal candidate is proactive, adaptable, and excited to contribute within a fast-paced biotechnology environment focused on advancing transformative genetic medicines for patients. Key Responsibilities - Provide operational and administrative support for global clinical studies across multiple gene therapy programs and study phases. - Support Trial Master File (TMF) management activities, including document collection, quality review, filing, reconciliation, and maintenance of inspection readiness. - Assist with clinical study start-up, maintenance, and closeout activities, including site documentation tracking, essential document management, investigator file support, and study communications. - Coordinate clinical meetings, including agenda development, meeting logistics, action item tracking, and preparation of meeting minutes. - Support vendor and CRO oversight activities, including tracking deliverables, invoices, contracts, purchase orders, and operational documentation. - Maintain clinical trial trackers, dashboards, study plans, timelines, enrollment reports, issue logs, and operational metrics. - Assist with investigator meeting planning, site training logistics, vendor meetings, and internal cross-functional study meetings. - Support regulatory and ethics submission preparation by coordinating required documentation and ensuring timely completion of deliverables. - Collaborate cross-functionally with Clinical Operations, Regulatory, Data Management, Safety, Quality, Medical Writing, and external partners to support efficient study execution. - Maintain clinical systems and databases, including CTMS, eTMF, document repositories, training records, and study-related operational tools. - Track study-related activities, deadlines, training assignments, and compliance requirements to support high-quality clinical trial execution. - Contribute to SOP development, process improvements, template management, and continuous operational excellence initiatives within the Clinical organization. - Ensure activities are conducted in compliance with GCP, applicable regulations, company policies, and quality standards. Qualifications - Bachelor’s degree in life sciences, healthcare, biology, nursing, public health, or related discipline preferred. - 1–4 years of experience supporting clinical research, clinical operations, pharmaceutical, biotechnology, CRO, academic research, or healthcare environments. - Experience supporting clinical trials or clinical operations activities strongly preferred. - Knowledge of clinical research regulations, ICH-GCP guidelines, clinical trial processes, and essential clinical documentation preferred. - Experience working with clinical systems such as CTMS, eTMF, Veeva Vault, Trial Interactive, Medidata, or related platforms preferred. - Strong organizational, project coordination, and multitasking skills with exceptional attention to detail. - Excellent written, verbal, and interpersonal communication skills. - Strong proficiency with Microsoft Office Suite (Excel, Word, Outlook, PowerPoint) and collaborative business tools. - Ability to manage multiple priorities and adapt effectively within a dynamic, fast-paced biotech environment. Additional Valued Qualifications - Experience in gene therapy, rare disease, neurology, oncology, cell therapy, biologics, or advanced therapeutics environments preferred. - Prior experience supporting outsourced clinical trial models and working with CROs, vendors, and clinical sites. - Exposure to global clinical studies and regulatory inspection readiness activities preferred. - Experience in emerging biotechnology or growth-stage life sciences companies 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.

• 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.

Role Description 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. 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. Qualifications - 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. Requirements - 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.

Title: Senior Manager HRIS, Benefits & Compliance Location: South San Francisco CA US Type: Full-time Workplace: Hybrid remote Job Description: The Senior Manager, HRIS, Benefits & Compliance is responsible for leading the strategy, administration, and continuous improvement of the company’s Human Resources Information Systems and employee benefits programs. This role serves as the primary owner of HR systems infrastructure and benefits operations, ensuring data integrity, system optimization, regulatory compliance, and an exceptional employee experience. As the organization continues to scale, this role will partner closely with People & Culture leadership, Finance, Payroll, IT, and external vendors to ensure HR systems and benefits programs support a growing and geographically distributed workforce. This position combines strategic planning with hands-on operational ownership and is expected to drive process improvements, system enhancements, and data insights that support organizational growth. This role reports to the Head of People & Culture. Open to candidates based in California or US remote. Key Responsibilities HRIS Strategy, Governance, and System Administration Own the overall administration, optimization, and governance of the company’s HRIS platform, including employee lifecycle transactions, workflows, reporting, and system configuration. In partnership with IT, develop and execute an HRIS roadmap that supports organizational scaling, evolving business needs, and future technology integrations. Serve as the primary system administrator responsible for maintaining system functionality, troubleshooting issues, managing upgrades, and coordinating system changes. Lead evaluation and implementation of new HR technologies, integrations, and automation opportunities that improve HR operations and employee experience. Ensure the accuracy, integrity, and security of employee data across HR systems. Partner with IT, Payroll, and Finance to maintain integrations between HRIS, payroll, equity administration, and other enterprise systems. Benefits Strategy and Administration Oversee the design, administration, and communication of employee benefits programs including medical, dental, vision, life, disability, wellness, retirement plans, and leave programs. Partner with leadership and external brokers to evaluate benefits strategy and ensure competitive offerings aligned with biotech industry benchmarks in the San Francisco Bay Area. Manage annual open enrollment planning, implementation, and employee communications. Act as the primary point of contact for benefits vendors, brokers, and third-party administrators. Provide guidance to employees regarding benefit programs, eligibility, and claims escalation when necessary. Compliance and Risk Management Ensure compliance with all applicable federal, state, and local regulations related to benefits administration and HR data management including ERISA, ACA, HIPAA, COBRA, and state leave programs. Maintain compliance with California-specific employment and benefits regulations including leave programs, pay transparency requirements, and reporting obligations. Oversee administration of employee leave programs including FMLA, CFRA, Pregnancy Disability Leave (PDL), California Paid Family Leave (PFL), ADA accommodations, and workers’ compensation coordination, partnering with third-party administrators and ensuring compliance with California and federal regulations while supporting employees and managers throughout the leave lifecycle. Support audits and reporting requirements related to HR systems and benefits programs. Maintain accurate plan documentation and required regulatory filings. Process Improvement and Operational Excellence Continuously evaluate HR systems and benefits processes to identify opportunities for automation, efficiency, and improved employee experience. Develop and maintain system documentation, standard operating procedures, and training resources. Provide training and guidance to HR team members and managers on HRIS functionality and benefits processes. Requirements Qualifications Bachelor’s degree in Human Resources, Business Administration, Information Systems, or related field. 10+ years of progressive experience in HRIS administration and benefits management, including experience in high-growth or scaling organizations. Experience supporting biotechnology, life sciences, or technology organizations strongly preferred, but not required. Strong experience administering modern HRIS platforms (e.g., ADP, Workday, UKG, Rippling, or similar). Demonstrated experience managing vendor relationships including benefits brokers and third-party administrators. Strong knowledge of employee benefits regulations and compliance requirements. Experience supporting multi-state employee populations, with strong knowledge of California employment and benefits regulations preferred. Advanced analytical and problem-solving skills with the ability to translate HR data into actionable insights. Strong communication and cross-functional collaboration skills. Preferred Qualifications HRIS, benefits, or HR certification such as CEBS, CBP, SHRM-CP/SHRM-SCP, or SPHR. Experience supporting HRIS implementations, system migrations, or major upgrades. Experience working in companies with fewer than 500 employees or in rapid growth environments. Compensation For candidates based in the SF Bay Area, the expected base salary range for this role is $170,000 - 205,000 For candidates based outside the SF Bay Area, the expected base salary range for this role is 150,000 - 180,000 The actual base pay offered will depend on factors such as experience, skills, and location. Employees in this role are also eligible to participate in our annual bonus and stock option program. 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 kitchen - Fitness center at our SF office - 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.

Role Description The Senior Manager, HRIS, Benefits & Compliance is responsible for leading the strategy, administration, and continuous improvement of the company’s Human Resources Information Systems and employee benefits programs. This role serves as the primary owner of HR systems infrastructure and benefits operations, ensuring data integrity, system optimization, regulatory compliance, and an exceptional employee experience. As the organization continues to scale, this role will partner closely with People & Culture leadership, Finance, Payroll, IT, and external vendors to ensure HR systems and benefits programs support a growing and geographically distributed workforce. This position combines strategic planning with hands-on operational ownership and is expected to drive process improvements, system enhancements, and data insights that support organizational growth. This role reports to the Head of People & Culture. Open to candidates based in California or US remote. Key Responsibilities - HRIS Strategy, Governance, and System Administration - Own the overall administration, optimization, and governance of the company’s HRIS platform, including employee lifecycle transactions, workflows, reporting, and system configuration. - In partnership with IT, develop and execute an HRIS roadmap that supports organizational scaling, evolving business needs, and future technology integrations. - Serve as the primary system administrator responsible for maintaining system functionality, troubleshooting issues, managing upgrades, and coordinating system changes. - Lead evaluation and implementation of new HR technologies, integrations, and automation opportunities that improve HR operations and employee experience. - Ensure the accuracy, integrity, and security of employee data across HR systems. - Partner with IT, Payroll, and Finance to maintain integrations between HRIS, payroll, equity administration, and other enterprise systems. - Benefits Strategy and Administration - Oversee the design, administration, and communication of employee benefits programs including medical, dental, vision, life, disability, wellness, retirement plans, and leave programs. - Partner with leadership and external brokers to evaluate benefits strategy and ensure competitive offerings aligned with biotech industry benchmarks in the San Francisco Bay Area. - Manage annual open enrollment planning, implementation, and employee communications. - Act as the primary point of contact for benefits vendors, brokers, and third-party administrators. - Provide guidance to employees regarding benefit programs, eligibility, and claims escalation when necessary. - Compliance and Risk Management - Ensure compliance with all applicable federal, state, and local regulations related to benefits administration and HR data management including ERISA, ACA, HIPAA, COBRA, and state leave programs. - Maintain compliance with California-specific employment and benefits regulations including leave programs, pay transparency requirements, and reporting obligations. - Oversee administration of employee leave programs including FMLA, CFRA, Pregnancy Disability Leave (PDL), California Paid Family Leave (PFL), ADA accommodations, and workers’ compensation coordination, partnering with third-party administrators and ensuring compliance with California and federal regulations while supporting employees and managers throughout the leave lifecycle. - Support audits and reporting requirements related to HR systems and benefits programs. - Maintain accurate plan documentation and required regulatory filings. - Process Improvement and Operational Excellence - Continuously evaluate HR systems and benefits processes to identify opportunities for automation, efficiency, and improved employee experience. - Develop and maintain system documentation, standard operating procedures, and training resources. - Provide training and guidance to HR team members and managers on HRIS functionality and benefits processes. Qualifications - Bachelor’s degree in Human Resources, Business Administration, Information Systems, or related field. - 10+ years of progressive experience in HRIS administration and benefits management, including experience in high-growth or scaling organizations. - Experience supporting biotechnology, life sciences, or technology organizations strongly preferred, but not required. - Strong experience administering modern HRIS platforms (e.g., ADP, Workday, UKG, Rippling, or similar). - Demonstrated experience managing vendor relationships including benefits brokers and third-party administrators. - Strong knowledge of employee benefits regulations and compliance requirements. - Experience supporting multi-state employee populations, with strong knowledge of California employment and benefits regulations preferred. - Advanced analytical and problem-solving skills with the ability to translate HR data into actionable insights. - Strong communication and cross-functional collaboration skills. Preferred Qualifications - HRIS, benefits, or HR certification such as CEBS, CBP, SHRM-CP/SHRM-SCP, or SPHR. - Experience supporting HRIS implementations, system migrations, or major upgrades. - Experience working in companies with fewer than 500 employees or in rapid growth environments. Compensation - For candidates based in the SF Bay Area, the expected base salary range for this role is $170,000 - 205,000. - For candidates based outside the SF Bay Area, the expected base salary range for this role is $150,000 - 180,000. - The actual base pay offered will depend on factors such as experience, skills, and location. - Employees in this role are also eligible to participate in our annual bonus and stock option program. 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 kitchen. - Fitness center at our SF office. - 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. Company Description 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.