Senior Scientist, Protein Engineering — Platform Discovery

Flagship Pioneering; Cambridge (MA); On-site; USD 126,000 - 182,000; Full time

Benefits offered by this job

Early employee equity stake

Custom-tailored role

Weekly lunches and community events

Job summary

Flagship Labs 129 (FL129) seeks a Senior Scientist to lead development of a novel platform for large‑scale protein variant libraries. You will design, build, and optimize deep mutational scanning workflows, and spearhead genotype–phenotype linking with advanced display systems and sequencing.

You will work closely with a multidisciplinary team, influence scientific direction, and own critical experimental strategies from day one in a fast‑moving biotech startup.

Qualifications

• Ph.D. in molecular biology, biochemistry, protein engineering, or a related field.
• 5+ years of industry or postdoctoral experience in relevant areas.
• End-to-end expertise in deep mutational scanning or library-scale mutagenesis.
• Hands-on library-scale cloning and mutagenesis.
• Experience with protein display systems and FACS workflows.
• NGS experience including amplicon sequencing and long reads.
• Protein expression, purification, and bioactivity assays.

Responsibilities

• Design, construction, and testing of large-scale protein variant libraries.
• Develop and optimize display, selection, and sorting workflows linking genotype to phenotype.
• Assess library quality, coverage, and validate outputs biochemically.
• Translate data into insights and present results to the team.
• Drive rapid, accurate data turnarounds to meet project goals.
• Set technical direction as an early member of the team.

Skills

Deep mutational scanning

Library-scale mutagenesis

Protein display systems

FACS

NGS data analysis

Protein expression & purification

Machine learning for protein eng

Team collaboration

Education

Ph.D. in molecular biology/biochemistry/protein engineering

Tools

Yeast display

Mammalian display

Phage display

Illumina/PacBio sequencing

Job description

Flagship Labs 129 (FL129) seeks a Senior Scientist to lead development of a novel platform for large‑scale protein variant libraries. You will design, build, and optimize deep mutational scanning workflows, and spearhead genotype–phenotype linking with advanced display systems and sequencing.

You will work closely with a multidisciplinary team, influence scientific direction, and own critical experimental strategies from day one in a fast‑moving biotech startup.