Flagship Pioneering is a scientific innovation engine that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps in human health, sustainability, and beyond. 

What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our team of scientists, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and create breakthroughs for the benefit of people and planet.
Many of the companies Flagship has founded 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 named four times to Fast Company’s annual list of the World’s Most Innovative Companies.

Role Overview

This is a high‑impact role at the intersection of science, strategy, and business, focused on shaping and advancing a differentiated BioMedicines R&D portfolio from early discovery through clinical development and commercialization readiness.

The role partners closely with senior BioMedicines and Flagship Pioneering leadership to define portfolio direction, build new R&D programs, and drive high‑stakes investment and prioritization decisions. You will work hands‑on with scientific leaders, internal venture teams, and partnering colleagues to translate complex science into clear strategies, executable plans, and compelling executive narratives.

Success in this role requires a roll‑up‑your‑sleeves mindset—owning analyses, building materials, structuring decisions, and moving work forward in a fast‑paced, ambiguity‑rich environment.

What You’ll Do

• Shape portfolio strategy and investment decisions across the BioMedicines pipeline, from preclinical inception through development
• Build and advance new R&D programs, defining development paths, milestones, resourcing plans, and decision points
• Develop integrated investment cases that synthesize scientific rationale, development feasibility, execution risk, and value creation
• Lead portfolio reviews, scenario planning, and trade‑off analyses (e.g., indication selection, timing, resourcing, probability‑adjusted value)
• Evaluate internal and external opportunities, including scientific, technical, strategic, and operational diligence of prospective assets
• Identify portfolio risks, gaps, and opportunities and recommend actions such as acceleration, de‑prioritization, partnering, or termination
• Translate complex scientific, clinical, and financial information into concise, executive‑level insights and decision materials
• Collaborate across R&D, Clinical Development, Regulatory, CMC, Finance, Commercial, Partnering, and internal venture teams
• Work directly with senior scientific and executive leaders (e.g., CSOs, CMOs, CBOs) to create and execute new programs
• Support governance and decision‑making forums that enable speed, clarity, and accountability
• Contribute to special strategic initiatives with the Head of Global Initiatives and SVP, Global Initiatives

Who You Are

You are a scientifically trained strategist who thrives at the boundary of deep science and structured problem‑solving. You are comfortable operating with senior leaders and equally comfortable doing the work yourself—from framing questions to building analyses and influencing decisions.

Qualifications

• PhD or MD in Life Sciences or a related field
• 5+ years of experience in management consulting (strategy and/or life sciences), biotech venture creation or investing, biopharma portfolio strategy, or related roles
• Strong understanding of biopharma R&D, clinical development, and regulatory pathways
• Experience working across multiple programs and stages of drug development
• Demonstrated experience with portfolio construction, scenario planning, and risk‑adjusted decision‑making
• Exceptional ability to synthesize complex data and communicate clearly with executives
• Proven ability to influence senior scientific and business leaders without formal authority
• Experience within the Flagship ecosystem is strongly valued

Equal Opportunity Employer

Flagship Pioneering is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, or protected veteran status. 

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The salary range for this role is $172,000 - $236,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.

THE ROLE 

As an Associate or Senior Associate at Flagship Pioneering in Molly Gibson’s Pioneering Business Unit (PBU), you will ideate, research, and refine novel venture hypotheses, validate key underlying unknowns of biology or technology and transition pressure-tested ideas into building a NewCo around the science.  You will help drive every facet of company origination from the early stages including identification and recruitment of critical partners and advisors, establishment of foundational IP, hiring and leadership of the early scientific team, and establishment of working norms and culture for the team.  In this role you will partner with stakeholders across the broader Flagship ecosystem to bring the full experience of Flagship to support your companies.  A successful candidate will become the expert on the foundational science of the company, frame and clearly communicate the strategy, and translate that strategy into a plan and lead operationalization of that plan alongside a Principal or Partner on the venture creation team. 

THE COMPANY 

Flagship Pioneering is a scientific innovation engine that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps in human health, sustainability, and beyond. 

What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our team of scientists, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and create breakthroughs for the benefit of people and planet.
Many of the companies Flagship has founded 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 named four times to Fast Company’s annual list of the World’s Most Innovative Companies.

KEY RESPONSIBILITIES 

• Contribute to and lead Flagship model explorations to rapidly assess interesting areas of science and develop novel, actionable and high value venture hypotheses 

• Outline key scientific questions to enable venture hypotheses and develop experimental plans to rapidly create value and pressure test ideas 

• Identify, build, and maintain relationships with appropriate academic KOLs and thought experts, ie, introducing them to the Flagship model, getting early buy-in, vetting/validation and de-risking key concepts of venture hypotheses 

• Understand IP landscape, formulate initial strategy, and write seminal applications for the technology and company. Assess patentability of existing IP landscape, including of key competitors and of potentially licensable estate 

• Develop corporate strategy and operations plan for the company. Define value creation, identify application spaces, build out organizational chart, define company goals, timelines and resourcing and identify strategic inflection points to set the company on the path to rapid growth and success 

• Develop audience-specific pitches for company 

• Support business development activities and continue to evolve the story 

• Manage and coordinate early scientific and IP employees. Source, recruit and manage KOLs and early-stage employees as well as relationships with CROs. 

• Manage & lead scientific team (internal or external) and daily research. Manage operational tasks, including establishing lab facilities, purchasing, HR, real estate acquisition, etc. 

• Become institutional subject matter expert and transfer to active company team. Stay up to date on the literature, conferences, funding opportunities, and new developments. 

• Work closely with and leverage Flagship operations teams (Finance, IP, IT, HR, and Talent) expertise for maximal operational excellence 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS  

The ideal candidate has a STEM-based PhD or MD from a top university and 2 or more years of experience in life sciences biotech, start-up or entrepreneurial activities. The candidate must have a passion for novel science and be operationally savvy. 

 Important skills and capabilities include: 

• Proven ability to rapidly become conversant in new areas of science and capable of engaging thought leaders at the deepest level of technological understanding 

• Ability to define a clear and compelling value proposition of a given scientific opportunity and effectively and cogently communicate that to technical and non-technical audiences 

• Basic understanding of multiple therapeutic modalities of drug discovery including small molecule, ADC, and protein therapeutics 

• Excellent analytical skills and ability to synthesize & communicate complex information rapidly and effectively 

• Energetic self-starter with strong presence and the ability to work effectively in an entrepreneurial environment 

• Open, transparent communication style and demonstrated willingness to engage in difficult conversations in a professional and productive manner 

• Passion for growth and development, with clear demonstration of openness to both giving and receiving feedback and track record of acting on feedback 

• Able to work effectively and pleasantly in teams with demonstrated abilities to lead and manage 

• Unmatched sense of urgency 

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.

 More About Flagship Pioneering:

We are creative optimists, and we would love for you to consider joining our team!  See all our open opportunities across Flagship Pioneering’s Ecosystem!

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, the firm has applied a unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, resulting in over $34 billion in aggregate value. To date, Flagship is backed by more than $4.4 billion of aggregate capital commitments, of which over $1.9 billion has been deployed toward the founding and growth of its pioneering companies alongside more than $10 billion of follow-on investments from other institutions. The current Flagship ecosystem comprises 41 transformative companies, including:  Axcella Health (NASDAQ: AXLA), Denali Therapeutics (NASDAQ: DNLI), Evelo Biosciences (NASDAQ: EVLO),  Foghorn Therapeutics, Indigo Ag, Kaleido Biosciences (NASDAQ: KLDO), Moderna (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY), Sana Biotechnology, Seres Therapeutics (NASDAQ: MCRB), and Syros Pharmaceuticals (NASDAQ: SYRS).

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The salary range for this role is $155,000 - $190,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health and sustainability exponentially accelerate scientific progress in areas ranging from cancer detection and treatment to nature-positive agriculture.

What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.
Many of the companies Flagship has founded 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.

Position Summary:

The Senior Facilities Manager will oversee maintenance and upkeep of equipment, machinery, general office area and the newly created Flagship Labs Watertown location.  This position will report to the Senior Director, Facilities and GMP Engineering Operations but will communicate with many stakeholders across the organization.  They will provide day-to-day support for lab and facilities operations by overseeing maintenance tasks under general guidance and will ensure continued compliance to cGXPs. This person will act as the single point of contact from a facilities infrastructure point of view to all Flagship Pioneering tenants within the building. Effective communication will be expected across all organizations and levels with “best in class” being the expectation of service. 

Responsibilities:

• Establishes vision for Facilities, providing hands-on leadership and development of team; oversees execution of Facility Operations.
• Effectively develops and leads site services with accountability for execution of site capital projects, process control automation, plant maintenance and site maintenance to enable Flagship Labs operations and other support functions to meet or exceed business expectations in cost, quality, compliance, safety, culture and capital.
• Maintains up to date records for all state, federal, and local licenses and inspections and maintains systems in compliance with local and state regulatory bodies associated with wastewater, sewer, emissions, waste handling/storage and disposal.
• Oversees overall facility and laboratory safety process
• Participates in facility design team meetings, provides visibility to senior management on progress and timelines. Manages general contractor and quality of build.
• Develops, implements, and maintains system/program for cGXP equipment maintenance and calibration; generates and revises SOPs, deviations and change controls associated with Facilities’ systems.
• Manages calibration, preventative and corrective maintenance of all GXP equipment, lab equipment, and building support utilities either directly or indirectly through contractor management; utility systems inclusive of but not limited to compressed gases, HVAC systems, electrical, life safety, and emergency power system (UPS).

Basic Qualifications:

• Bachelor’s Degree is preferred.
• 7+ years of experience in a regulated environment, with 5+ years of Facility maintenance or Engineering experience.
• Direct experience maintaining large scale mechanical systems (HVAC/Refrigeration/Vacuum/Compressed Gases).
• Lab Design, Operation and Maintenance is a plus.
• Knowledge of local and state regulatory requirements related to wastewater, emissions, sewer systems, waste handling/storage and disposal.
• Strong technical writing skills; Ability to work independently, with minimal supervision.

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.

#LI-NM1

The salary range for this role is $128,000 - $176,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Flagship Pioneering currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.