Senior Scientist, Protein Assay Development and Screening

Flagship Pioneering, Inc.•Cambridge, MA

About The Position

FL116, backed by Flagship Pioneering, is an early-stage biotechnology company transforming the way biomolecules are synthesized. Our innovative platform has the potential to transform the way these critical research, diagnostic, and therapeutic tools are manufactured. We are seeking passionate problem solvers ready to make a profound impact on biotechnology and therapeutic innovation. Position Summary We are seeking a creative, motivated, and technically exceptional Senior Scientist to lead high-throughput protein expression and assay development. This role will focus on building scalable, manual and automated workflows for rapid protein generation and functional screening, and integrating those outputs into a design-build-test-learn (DBTL) cycle that powers our platform. The ideal candidate is a hands-on experimentalist who thrives in a fast-paced, team-oriented environment and is driven by solving hard problems with elegance and speed.

Requirements

D. in Biochemistry, Protein Engineering, Synthetic Biology, Molecular Biology, or related discipline, with 5+ years of relevant industry experience.
Hands-on expertise in high-throughput protein expression (bacterial and/or cell-free systems) and purification.
Strong track record of designing and executing quantitative protein assays at scale.
Experience handling, analyzing, and interpreting large biological datasets.
Demonstrated ability to work collaboratively in a dynamic, fast-paced environment.
Clear and concise communicator with excellent organizational and problem-solving skills.
Proficiency in protein and nucleic acid characterization techniques (LabChip, platereader, gel electrophoresis, TapeStation/Fragment Analyzer, sequencing technologies, Mass Spectrometry)

Responsibilities

Develop scalable high-throughput expression systems in coli and cell-free formats for protein production across diverse constructs and libraries.
Design and implement multiplexed protein screening assays using plate-based readouts (e.g., fluorescence, luminescence, absorbance), mobility-based platforms (e.g., LabChip, TapeStation), and other automated methods.
Generate and analyze large experimental datasets to extract actionable insights, inform platform improvements, and feed downstream ML models.
Collaborate closely with cross-functional partners, including machine learning scientists, chemists, and biochemists, to ensure cohesive integration across the platform.
Contribute to team building, lab infrastructure, and the overall strategic direction of the team.
Document experimental results rigorously, communicate clearly, and present findings effectively to internal and external stakeholders