FL129 | Cambridge, MA Senior Scientist, Protein Engineering

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

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

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.

Position Summary:

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. Deep experience with protein display systems, high‑throughput sorting, and sequencing‑based readouts is essential, and familiarity with bioinformatic analysis of variant‑level data is strongly desired. The ideal teammate will be highly adaptable, have strong organizational and communication skills, and will thrive in a highly collaborative and multidisciplinary environment.

Key Responsibilities:

• Technology development, aligned with FL129’s core strategic goals. This role is among the first hires, and we’re looking for someone who thinks critically and will influence the company’s scientific direction.
• Design, construction, and experimental testing of 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 library outputs by biochemical and biophysical characterization of purified proteins
• Optimize existing workflows and establish best experimental and documentation practices to enable platform excellence.
• Ensuring rapid and accurate turnaround of data to drive achievement of key project goals.
• Translate experimental data into meaningful insights and present results at team meetings.

Preferred Qualifications:

• 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.
• Experience with protein expression and purification, and with biochemical/biophysical assay development to quality‑control library inputs and quantitate the bioactivity of library outputs.
• Nice to have: experience with machine learning methods for protein engineering, or with statistical analysis of variant fitness landscapes.
• Motivated team‑player and independent force‑of‑nature with strong organizational and written/verbal communication skills.

What we can offer you:

• 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.

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross‑functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL129 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL129's good faith estimate as of the date of publication and may be modified in the future.