# Senior Scientist, Protein Engineering at Flagship Pioneering

- Company: Flagship Pioneering
- What the company does: Pioneering Partnerships Latest News.
- Company website: https://www.flagshippioneering.com
- Type: VC firms
- Level: Senior
- Location: Cambridge, MA USA
- Work setup: On-site
- Pay: $126K to $182K base salary per year (USD)
- Posted: 2026-09-08
- Apply by: 2026-10-23
- Apply: https://boards.greenhouse.io/flagshippioneeringinc/jobs/8784082002?gh_jid=8784082002
- Page: https://www.1752.vc/careers/jobs/flagship-pioneering-senior-scientist-protein-engineering/

## About the role

We are seeking a motivated and highly collaborative Senior Scientist to join FL129’s growing team of experimental and computational scientists to build a novel platform technology. The successful candidate will have a strong track record of scientific and technical innovation in the design, construction, and functional interrogation of large protein variant libraries, including deep mutational scanning and related library-scale methods.

## What they're looking for

- Ph.D. in molecular biology, biochemistry, protein engineering, or a similar field with 5+ years of industry or postdoctoral experience
- End-to-end experience with deep mutational scanning or related library-scale mutagenesis methods, from variant library design and construction through selection, sequencing, and variant-level data analysis
- Hands-on expertise in library-scale molecular cloning, including site-saturation or degenerate-codon mutagenesis, high-efficiency transformation, and managing library complexity, variant coverage, and bottlenecking
- Experience with protein display systems that link genotype to phenotype, such as yeast surface display (YSD), 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 (NGS) technologies (Illumina and PacBio), including amplicon sequencing and long-read approaches for variant–barcode linkage, and ideally single-cell sequencing technologies

Tags: Biological Engineering