Pioneering Medicines: Senior / Principal Scientist, Compound Management

Flagship Pioneering•Cambridge, MA

About The Position

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 . 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.

Requirements

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.

Nice To Haves

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

Responsibilities

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.
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.
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.