FL129 | Cambridge, MA Senior Scientist, Protein Engineering

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

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Benefits package

Job summary

Flagship Pioneering seeks a Senior Scientist for FL129 to design, construct, and interrogate large protein variant libraries, linking genotype to phenotype at scale. You will shape technical strategy as an early hire and help build the team while collaborating with computational and screening colleagues.

We welcome candidates from deep mutational scanning, directed evolution, protein display engineering, and related fields who are excited to translate readouts into data products powering the

Qualifications

• Ph.D. in molecular biology, biochemistry, protein engineering, or related field with 5+ years of experience.
• Hands-on library-scale cloning including saturation mutagenesis and high-efficiency transformation.
• Experience with display systems linking genotype to phenotype.
• Experience with FACS and design of sort gates for enrichment.
• Experience with NGS readouts for variant analysis.
• Strong communication and collaboration skills.

Responsibilities

• Set technical direction for library design and functional interrogation.
• Design, construct, and test large-scale protein variant libraries.
• Establish display, selection, and sorting workflows linking genotype to phenotype.
• Assess library quality and validate outputs via biochemical/biophysical assays.
• Build and evolve the protein-engineering function and workflows.
• Collaborate with computational teams to translate readouts into data products.
• Translate data into insights and present results to the team.

Skills

Molecular biology

Biochemistry

Protein engineering

Library-scale cloning

FACS

NGS readouts

Team collaboration

Education

Ph.D. in a relevant field

Tools

Yeast display

Mammalian display

Phage display

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 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.

Key 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.

Must-have Qualifications

• 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.

Preferred Qualifications

• Protein expression and purification, with biochemical/biophysical assay development to QC library inputs and quantify 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.

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.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].