Pioneering Medicines: Senior / Principal Scientist, Compound Management

What if…

We could harness the power of Flagship’s breakthrough scientific platforms to create entirely new therapeutic modalities — and deliver transformative medicines to patients faster?

Pioneering Medicines, a division of Flagship Pioneering, is building a premier biopharmaceutical R&D organization dedicated to conceiving and advancing life-changing therapies. By integrating and applying Flagship’s innovative platform technologies to serious diseases with high unmet need, we aim to redefine how medicines are discovered and developed. A defining strength of our approach is the ability to combine multiple platforms to generate truly novel and potentially transformative treatments.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation company that conceives, creates, resources, and develops first-in-category scientific ventures to transform human health and sustainability. Since its founding in 2000, Flagship has originated and fostered more than 100 scientific ventures, generating tens of billions in aggregate value and advancing breakthroughs across biotechnology and sustainability. Flagship’s unique hypothesis-driven innovation model has enabled the creation and growth of an ecosystem of 40+ companies — including high-impact ventures such as Moderna, Tessera Therapeutics, Generate:Biomedicines, Sana Biotechnology, Indigo Agriculture, and Inari — that span cutting-edge platform technologies and therapeutic modalities

Position Summary:

We are seeking a Compound Manager at Senior Scientist/ Principal Scientist level to join our rapidly evolving Sample Operations and Automation function. This individual will collaborate with operational and scientific teams to manage the registration, storage, and distribution of small molecules, peptides, biologics and additional modalities, while leading the automation of liquid handling, serial dilutions, and assay plate dispensing workflows at Pioneering Medicines. In addition, the individual will collaborate with Information Technology to streamline data collection, analysis, and storage workflows.

The successful candidate will combine deep operational expertise with a hands-on approach to automation and process development, ensuring high-quality, reproducible data from early discovery programs across multiple therapeutic areas and modalities.

Key Responsibilities:

Compound and Sample Management

• Oversee end-to-end compound management workflows through collaboration with the lab operations team, including receipt, registration, storage, tracking, and distribution of small molecules, peptides, biologics, nucleic acids, and other modalities across Pioneering Medicines’ research programs.
• Maintain sample integrity and traceability through robust documentation, inventory systems and adherence to SOPs.
• Manage compound collections in proper storage systems (ambient, refrigerated, cryogenic), and ensure environmental compliance and monitoring, in collaboration with the laboratory operations group.

Automation and Workflow Execution

• Partner with team members to operate, program, and maintain automated liquid handling systems (e.g., Agilent Bravo, Dispendix I.DOT) for high-throughput sample preparation.
• Develop, validate, and optimize serial dilution, reformatting, and assay plate dispensing methods to enable high throughput assays and profiling campaigns.
• Implement automation scheduling software (e.g., VWorks) to coordinate workflows and maximize throughput.
• Drive continuous improvements in automation reliability and process standardization.

Data and Informatics Integration

• Interface with informatics platforms (e.g., CDD Vault, Benchling, and compound databases) to ensure accurate data capture and seamless sample tracking.
• Collaborate with data science teams to link sample metadata with experimental results for analytical and decision-support workflows.
• Generate and maintain inventory, utilization, and QC reports across multiple program portfolios.

Qualifications:

Required:

• Bachelor’s or Master’s degree in Chemistry, Biochemistry, Chemical Engineering, or related discipline with 12+ years of experience.
• Strong experience in compound management within pharma, biotech, or high-throughput discovery environments.
• Demonstrated proficiency with liquid handling platforms and compound inventory management systems.
• Deep understanding storage considerations for diverse modalities (e.g., small molecules, peptides, biologics).
• Proven ability to troubleshoot, optimize, and document automated workflows.
• Strong organizational and communication skills, with the ability to manage multiple priorities in a dynamic environment.

Preferred:

• Experience in multi-modal sample management (e.g., nucleic acids, conjugates).
• Prior exposure to early-stage R&D or platform company operations.

Core Competencies:

• Operational excellence and meticulous attention to detail
• Strong technical troubleshooting and analytical mindset
• Collaborative and adaptable in a fast-evolving environment
• Commitment to innovation, data integrity, and process improvement
• Excellent written and interpersonal communication

 

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.

 

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.

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The salary range for this role is $126,000 - $214,500. 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.