FL129 | Cambridge, MA Senior Scientist, Discovery Technologies

Flagship Pioneering; Cambridge (MA); On-site; USD 126,000 - 181,500; Full time

Benefits offered by this job

Weekly lunches

Monthly social events

Snacks and coffee

Job summary

Flagship Pioneering in Cambridge, MA is seeking a Senior Scientist to build a novel platform for small molecule discovery. You will join FL129’s team of experimental and computational scientists, shaping the platform and its scientific direction.

The role emphasizes collaboration, adapting screens to protein targets, and advancing data-driven insights across teams with strong communication and organizational skills. This is an early-stage opportunity with significant scientific impact.

Qualifications

• Ph.D. in molecular biology, systems biology, chemical biology, or a similar field with 5+ years of experience.
• End-to-end experience with small molecule screening from library design to sequencing and data analysis.
• Experience managing contract research organizations (CROs).
• Nice to have: cheminformatics, on-DNA/off-DNA validation, surface display, single-cell/genomics.
• Motivated team-player with strong written and verbal communication skills.

Responsibilities

• Technology development aligned with core strategic goals; contribute to scientific direction.
• Design, construct, and test target/variant libraries with binding assays.
• Optimize workflows and establish best practices for platform excellence.
• Ensure rapid and accurate data turnaround to meet project goals.
• Translate data into insights and present results to the team.

Skills

Strong communication

Organizational skills

Cross-functional collaboration

Education

Ph.D. in molecular biology, systems biology, chemical biology, or similar

Tools

DNA tagging optimization

Next-generation sequencing

Cheminformatics

Job description

Senior Scientist, Discovery Technologies

Cambridge, MA USA

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 develop a technology tofacilitatethe data generation necessary for training the next generation of generative chemistry models 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 andknow-howof Flagship Pioneering.

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 strong track record of scientific and technical innovation in molecular biology and small molecule screening, including experience adapting screens to cell- or surface-displayed protein targets. Additional experience with or exposure to yeast surface display, single-cell or genomics methods, and cheminformatics are preferred. 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, andwe’relooking for someone who thinks critically and will influence the company’s scientific direction.
• Design, construction, and experimental testing of custom target/variant libraries, including binding assays against cell- or surface-displayed protein targets
• Optimizeexisting workflows andestablishbest experimental and documentation practices to enable platform excellence.
• Ensuring rapid andaccurateturnaround 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,systems biology,chemical biology, or a similar field with 5+ years of industry or postdoctoral experience.
• End-to-end experience withsmall molecule screening from library design, including optimization of DNA tags for amplification,quantitationand sequencing, toscreening, next-gensequencing, to data analysis.
• Experience managing contract research organizations (CROs).
• Nice tohave:cheminformatics experience, on-DNA and off-DNA hit validation experiencewith DNA-encoded positive control and library compounds,surface display technologies, droplet-based screening and/or microfluidics,and single-cell or genomics methods.
• 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 communicationskills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will becommensuratewith 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, genderidentityor 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 your 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].

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.