Senior Director, Project and Alliance Management

Prologue Medicines, a Flagship Pioneering company, is building a new class of medicines from the viral proteome: the millions of proteins viruses have evolved to engage and regulate human biology. Its DELVE platform combines a viral-protein knowledge graph and computational design with high-throughput, automated testing to discover, characterise and engineer novel proteins with potential across many therapeutic areas.

We are seeking a Senior Director, Project & Alliance Management to drive cross-functional execution of programs from preclinical development through IND/CTA submission, first-in-human studies, and early clinical development, while ensuring effective governance of strategic partnerships.

Key Responsibilities

Project & Program Management (Preclinical through Clinical)

• Lead cross-functional project management for programs from discovery and preclinical through IND-enabling work and into the clinic, owning integrated timelines, deliverables, risks and resource needs.
• Demonstrated experience leading cross-functional development programs through IND/CTA-enabling activities, regulatory submission, and transition into clinical development.
• Build and maintain development plans, milestones, decision points and risk registers with scientific, translational, CMC, regulatory, clinical and operations leaders; track dependencies across discovery, platform, development and alliance activities.
• Run program team meetings and stage-gate reviews so decisions are documented and actions are owned; coordinate CRO/CDMO planning and oversight with functional owners.
• Anticipate development challenges, evaluate tradeoffs, and drive timely cross-functional decisions to maintain program momentum.
• Give executive leadership candid, consistent visibility into status, critical path and tradeoffs.

Alliance Management

• Serve as primary operational lead for strategic partnerships, aligning on objectives, responsibilities, milestones, decision rights and governance.
• Lead Joint Steering Committees and other alliance forums: agendas, briefing materials, decision tracking and follow-through.
• Translate collaboration agreements into operating plans; track obligations, deliverables, milestone and option events, and amendments.
• Monitor alliance health, risks and dependencies, escalating with a recommended path forward; give operational input to negotiations with legal, finance and business development.
• Manage alliance information flow, including data sharing and reporting obligations, and build trusted partner relationships.

Resource, Time & Portfolio Tracking

• Implement and own time tracking for project teams, giving a consistent view of effort by program, workstream, alliance and activity, while keeping it simple and low-burden for scientists.
• Use the data for resource planning, capacity forecasting, FTE and budget reconciliation, portfolio prioritization and, where agreements require, alliance cost-sharing and reporting with finance.
• Maintain portfolio dashboards covering timelines, milestones, resourcing and risk across all programs and alliances.

Strategic Leadership

• Partner with executives on portfolio prioritization, program sequencing, alliance strategy and resource allocation.
• Build scalable governance frameworks, tools and reporting processes; drive continuous improvement and accountability internally and with partners.
• Represent the function in internal planning and external partner forums; as the team grows, hire and develop talent.

Required Qualifications

• PhD, MS or MBA in life sciences or a related field, with 5+ years working closely with scientific teams in biotech or pharma.
• 10–15+ years in biotech or pharma project/program, alliance or portfolio management, or related operational leadership.
• Hands-on cross-functional project leadership across both preclinical and clinical development, ideally taking a program through IND/CTA into the clinic.
• Demonstrated success managing complex external partnerships, including joint governance (JSC/JPT), contractual obligations and multi-stakeholder relationships.
• Strong grasp of drug development, scientific operations and alliance execution in biotech.
• Proficiency with planning tools (e.g., Smartsheet) and experience with time/effort tracking and resource management.
• Proven ability to influence without authority, resolve conflict and drive accountability across matrixed teams.
• Excellent communication and facilitation skills; thrives in a lean, entrepreneurial environment with shifting priorities.

Preferred Qualifications

• Programs spanning preclinical and clinical development, including Phase 1/2 execution.
• Alliances involving scientific, legal, finance and executive stakeholders, including alliance financials and milestone tracking.
• Building governance frameworks, program tools and reporting processes in a growing biotech.
• Novel modalities or platform-enabled programs (e.g., biologics, protein therapeutics, computationally driven discovery).
• Structured decision-making and executive governance in an early-stage biotech; PMP/PgMP or alliance management certification a plus.

The salary range for this role is $213,000 - $280,500.