Senior Scientist, Protein Engineering

Flagship Pioneering, Inc. • Cambridge, MA

3d • $126,000 - $181,500

About The Position

Flagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission: to unlock the future of small molecule drug discovery. FL129 is developing a revolutionary approach to this challenge and is recruiting a team of top-tier scientists to build this powerful and first-in-category platform. This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering. This is a hands-on role with substantial ownership for a scientist who is excited to set technical direction from day one and, over time, help build the team. We are seeking a motivated and highly collaborative Senior Scientist to join FL129's growing team of experimental and computational scientists building a novel platform technology. The successful candidate will design, construct, and functionally interrogate large protein variant libraries — linking variant genotype to measured phenotype at scale — and will help translate those readouts into data products that drive the platform. This role is among the first hires, affording the opportunity to shape and influence the company's scientific direction and team culture. We welcome candidates from a range of adjacent backgrounds — deep mutational scanning, directed evolution, antibody or protein display engineering, massively parallel reporter assays (MPRA), or pooled genetic screens — who have the core library-building and selection skills below and are energized by applying them to a new problem.

Requirements

• Ph.D. in molecular biology, biochemistry, protein engineering, or a related field, with 5+ years of industry or postdoctoral experience.
• Hands-on expertise in library-scale molecular cloning — site-saturation or degenerate-codon mutagenesis, high-efficiency transformation, and managing library complexity, variant coverage, and bottlenecking.
• Experience with a protein display or genotype-to-phenotype linkage system (e.g., yeast surface display, mammalian display, or phage display).
• Experience with fluorescence-activated cell sorting (FACS), including selection strategy and sort-gate design for quantitative variant enrichment.
• Experience with next-generation sequencing readouts for variant-level analysis (e.g., Illumina amplicon sequencing).
• A motivated team-player and independent force-of-nature with strong organizational and written/verbal communication skills.

Nice To Haves

• Protein expression and purification, with biochemical/biophysical assay development to QC library inputs and quantitate the bioactivity of library outputs.
• Familiarity with bioinformatic analysis of variant-level data.
• Exposure to machine learning methods for protein engineering or variant-effect prediction (e.g., ESM, variant-effect models), or statistical analysis of variant fitness landscapes.
• Prior experience as an early hire in a startup.

Responsibilities

• Set technical direction for library design and functional interrogation, aligned with FL129's core strategic goals, and influence the company's broader scientific strategy as an early hire.
• Design, construct, and experimentally test large-scale protein variant libraries, including deep mutational scanning and related saturation mutagenesis approaches.
• Establish and optimize display, selection, and sorting workflows that link protein genotype to measured phenotype.
• Assess library quality and variant coverage and validate outputs through biochemical and biophysical characterization of purified proteins.
• Build and evolve the protein-engineering function: optimize workflows and establish best experimental and documentation practices to enable platform excellence.
• Partner closely with computational and screening colleagues to turn experimental readouts into the data products that power the platform.
• Translate experimental data into meaningful insights and present results at team meetings.

Benefits

• Opportunity to lay the scientific foundation of a transformative platform company as an early employee.
• Custom-tailored role to maximize impactful contributions, professional growth, and scientific interests.
• Weekly lunches, monthly social events, and community lunchroom with free snacks, coffee, all embedded in a vibrant community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies.
• healthcare coverage
• annual incentive program
• retirement benefits

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree