Sr. Director, Alliance and Program Management

Flagship Pioneering; Cambridge (MA); On-site; USD 217,000 - 275,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering in Cambridge, MA is seeking a Senior Director, Alliance & Program Management to serve as an operational and strategic partner to the COO and program teams. The role emphasizes day-to-day alliance execution, governance, and building disciplined program management across a growing portfolio.

The ideal candidate has 10–15+ years in biotech/pharma alliance and program leadership, with hands-on experience leading multi-program portfolios and executive governance.

Qualifications

• Ph.D./MBA with biotech/pharma experience.
• 10–15+ years in alliance and program management.
• Experience managing external partnerships and governance.
• Leadership across matrixed biotech teams.
• Experience with portfolio planning and executive governance.

Responsibilities

• Lead alliance execution for strategic collaborations.
• Develop governance and operating plans for programs.
• Manage Joint Steering Committees and governance forums.
• Partner with BD to structure new alliances.
• Create portfolio dashboards and reporting for leadership.
• Support portfolio prioritization and strategic investment decisions.

Skills

Alliance management

Portfolio management

Program management

Stakeholder management

Strategic thinking

Cross-functional leadership

Education

Ph.D. in life sciences

MBA

Job description

Sr. Director, Alliance and Program Management

Cambridge, MA USA

Company Summary

ProFound™ Therapeutics is a biotechnology company discovering novel proteins across the expanded human proteome to unlock transformative drug targets and first-in-class medicines. The company’s proprietary ProFoundry™ Platform integrates state-of-the-art protein detection, validation, and computational technologies to systematically identify and characterize previously unknown proteins and validate their therapeutic potential. This approach has generated a rapidly expanding portfolio of novel targets and programs advancing toward the clinic, along with strategic collaborations with leading pharmaceutical partners. Together, these efforts support the development of breakthrough treatments across a broad range of disease areas. For more information, please visit www.profoundtx.com .

Position Summary

ProFound Therapeutics is seeking a Senior Director, Alliance & Program Management to serve as an operational and strategic partner to the Chief Operating Officer, leadership team, and program teams.

This role has two primary responsibilities: (1) serving as the day-to-day operational leader for ProFound's strategic pharmaceutical collaborations and (2) building the company's portfolio and program management capabilities. The role ensures successful alliance and program execution while developing the governance, planning processes, and operating systems that enable disciplined execution across the company's growing portfolio. This is a highly visible role requiring exceptional judgment, operational rigor, and the ability to influence without authority. The successful candidate will lead day-to-day alliance execution, enable governance, implement practical program management systems, and partner with scientific leadership to translate decisions into disciplined execution and ensure that programs remain aligned on objectives, timelines, budget, risks, and resource needs.

The ideal candidate is an experienced biotechnology operator who combines strategic thinking with hands‑on execution. They thrive in a lean, entrepreneurial environment where priorities evolve rapidly and success depends on bringing structure to complexity, building practical solutions, fostering collaboration, and driving accountability across highly matrixed teams.

Key Responsibilities

Alliance Management

• Serve as the primary Alliance Manager and operational leader for ProFound's strategic pharmaceutical collaborations, ensuring successful execution of scientific objectives, governance activities, and contractual commitments.
• Build trusted relationships across partner organizations while coordinating cross-functional scientific, legal, finance, IP, and operational teams to drive alliance execution.
• Lead Joint Steering Committees (JSCs) and other governance forums, ensuring meetings are well prepared, decisions documented, and actions successfully executed.
• Partner with Business Development to help structure new alliances for successful execution.
• Translate collaboration agreements into executable operating plans, proactively managing milestones, deliverables, risks, issues, and partner expectations.
• Monitor alliance health and performance, resolving conflicts constructively and providing executive leadership with clear visibility into key risks and opportunities.
• Build credibility through exceptional execution, proactive communication, sound judgment, and effective stakeholder management.

Program Management

• Build and continuously improve ProFound's portfolio and program management capabilities, including governance, tools, and operating processes.
• Lead integrated program management across discovery and early development programs, ensuring visibility into progress, risks, and resource needs.
• Train and support scientific teams in adopting practical project management tools and consistent execution practices.
• Partner with scientific leadership to implement stage-gate processes, governance frameworks, and portfolio reporting that support timely, high-quality decisions.
• Partner with Finance to integrate program plans, budgets, and decision points, framing up options for timely investment, tradeoff, and resource allocation decisions.
• Facilitate cross-functional program reviews, ensuring alignment, accountability, and effective follow-through on key decisions and actions.
• Foster an operating culture that balances executional discipline with the agility of a growing biotechnology company.
• Partner with executive leadership to drive portfolio prioritization, governance, and strategic investment decisions across pipeline and platform initiatives.
• Support annual strategic planning, Long‑Range Planning (LRP), and portfolio planning by coordinating program assumptions, milestones, timelines, and resource inputs.
• Develop executive dashboards and portfolio reporting that improve visibility into organizational priorities, execution, and performance.
• Provide program management support for executive governance meetings and other high-priority cross‑functional initiatives.

Qualifications

Experience

• Ph.D. or M.S. in life sciences, or MBA with at least 5 years of direct experience working closely with scientific teams in a biotech or pharmaceutical setting.
• 10-15+ years’ experience in biotech or pharma alliance management, portfolio management, program management, and operational leadership.
• Demonstrated success managing complex external partnerships, including governance, contractual obligations, and relationship management requiring judgement and influence across multiple stakeholders.
• Hands‑on experience leading program management across multi-program biotech portfolios, from early discovery through translational development.
• Proven track record of building portfolio management processes, governance models, and project management capabilities within a growing biotechnology company.
• Experience supporting portfolio prioritization, strategic planning, and executive governance.
• Experience working closely with scientific leadership and large pharma partners.

Capabilities

• Exceptional judgment and credibility, with a demonstrated ability to influence senior scientific leaders and external partners while navigating complex, cross‑organizational decisions.
• Outstanding operational rigor and systems thinking, with the ability to build practical governance processes, tools, and execution frameworks that improve accountability and visibility without creating unnecessary bureaucracy.
• Excellent communication and facilitation skills, translating complex scientific, operational, and business issues into clear decisions, action plans, and executive‑level communications.
• Proven ability to influence without authority, build consensus, proactively manage stakeholders, and drive accountability across highly matrixed organizations.
• Skilled at resolving conflict constructively, balancing diplomacy with accountability while building trusted relationships with internal teams and external partners.
• Highly organized and detail‑oriented, with the ability to seamlessly shift between execution details and strategic organizational priorities.
• Collaborative, low‑ego leader with a solutions‑oriented mindset and a demonstrated ability to build trust across functions and organizations.
• Thrives in lean, fast‑paced, entrepreneurial environments, demonstrating adaptability, resourcefulness, and a strong bias toward action.

Values and Behaviors

We are seeking leaders who demonstrate strategic thinking, extreme teamwork, executional excellence, adaptability, and a commitment to inclusion and diversity. We particularly value candidates who combine intellectual curiosity with a strong bias toward action - who are as comfortable asking a question as they are driving a workstream to close. We encourage candidates with passion, leadership capability, and depth across these functional areas - even if not meeting every requirement - to apply.

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com .

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer

All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies

Flagship Pioneering and its affiliated Flagship Lab companies (collectively, "FSP") do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $217,000 - $275,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. ProFound Therapeutics, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on ProFound Therapeutics, Inc.'s good faith estimate as of the date of publication and may be modified in the future.

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