Pioneering Medicines: Principal Scientist / Associate Director, Analytical Development

What if... We could harness the power of Flagship’s scientific platforms and create novel treatment options that benefit more patients, sooner?

About Pioneering Medicines:

Pioneering Medicines, Flagship Pioneering’s in-house drug development unit, is dedicated to conceiving and developing a broad portfolio of life-changing treatments for patients built from Flagship’s innovative platforms. Harnessing the drug development expertise of its team together with the power of Flagship's multiple scientific platforms, Pioneering Medicines explores and identifies new product concepts which are then advanced jointly with Flagship’s bioplatform companies. Within Flagship’s Innovation Supply Chain partnerships, Pioneering Medicines works with external collaborators to apply its unique approach to partners’ R&D priorities. These partnerships are highly co-creative strategic alliances that accelerate therapeutic innovation by bringing together partners spanning the full spectrum of drug discovery, development, and production.

Position Summary

We are seeking an experienced and collaborative Principal Scientist / Associate Director, Analytical Development to join our Technical Operations group. This role will support analytical development, analytical control strategy, QC oversight, and day-to-day analytical operations across multiple CMC programs.

Reporting to the Director of Analytical Development, this individual will serve as an analytical lead for in-house programs and partner closely with Formulation, Drug Substance, Drug Product, Quality, Regulatory, and broader CMC teams. The role will provide technical leadership within the growing team and across a global network of CDMOs and contract testing laboratories, ensuring analytical execution, regulatory compliance, and QC deliverables throughout the product lifecycle.

This position offers broad cross-functional exposure, analytical ownership and the opportunity to influence analytical strategy, regulatory content, and organizational growth within a dynamic biotechnology environment.

Key Responsibilities

Analytical Development & Lifecycle Management

• Support analytical method development, qualification, transfer, and lifecycle management for drug substance and drug product testing.
• Ensure methods are scientifically robust, phase-appropriate, and aligned with regulatory expectations.
• Contribute to specifications and control strategies across development stages.

QC Oversight & External Testing

• Lead and coordinate QC activities across programs to support cGMP compliance and project objectives.
• Oversee external testing for release, characterization, comparability, and stability studies.
• Serve as the technical liaison for CDMOs, CROs, and contract testing laboratories.

Data Review & Stability Programs

• Review, interpret, trend, and summarize analytical data from release and stability studies.
• Implement and support stability programs in accordance with regulatory expectations.
• Prepare technical summaries, stability assessments, and interim/final trending reports using appropriate scientific and statistical approaches.

Compliance, regulatory and quality support

• Author, review, and approve technical and GMP documents
• Maintain strong ALCOA based data integrity practices.
• Contribute to CMC sections for INDs and related regulatory submissions.
• Support responses to agency questions and information requests.
• Support continuous improvement of quality systems related to analytical testing and QC operations.

Cross-Functional Leadership

• Promote alignment of analytical strategies, quality expectations, and best practices across internal and external teams.
• Demonstrate scientific judgment, initiative, accountability, and the ability to influence cross-functional leaders in a matrixed environment.

Qualifications Required:

• A degree in Chemistry, Biochemistry, Biology, Pharmaceutical Sciences, or related discipline
• PhD with 8+; MS with 12+; BS with 14+ years of relevant industry experience
• Expertise in analytical development across diverse therapeutic modalities, including chromatographic, electrophoretic, immunological, binding, and potency-based methods.
• Demonstrated success developing, optimizing, qualifying, and implementing novel analytical methods to address complex and evolving program needs.
• Strong strategic understanding of characterization approaches for proteins, biologics, mAbs and other related modalities.
• Experience with other modalities including peptides and nucleic acids is desirable.
• Proven experience providing technical oversight of external CRO/CDMO analytical operations, including ICH-compliant stability programs and GMP testing activities.
• Experience developing, qualifying, and troubleshooting cell-based potency assays is highly desirable.
• Strong working knowledge of CMC regulatory expectations and analytical content required for global regulatory submissions.

Additional Skills

• Familiarity with statistical and data analysis tools such as JMP and Excel.
• Strong technical problem-solving, risk assessment, and scientific judgment.
• Excellent organizational and management skills with the ability to manage multiple priorities.
• Proven ability to author, review, and approve scientific and GMP documentation.
• Strong communication, collaboration, and influencing skills.

About Flagship

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.

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.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.

The salary range for this role is $148,000 - $203,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Medicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Medicines's good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.