Senior Scientist, Protein Engineering

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 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.

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.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto

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 privacy@flagshippioneering.com.

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 privacy@flagshippioneering.com.