Senior Research Associate, Molecular Biology and Sequencing

Flagship Pioneering; Cambridge (MA); On-site; USD 81,000 - 107,000; Full time

Job summary

Flagship Pioneering in Cambridge, MA is seeking a Senior Research Associate to own next-generation sequencing and high-throughput cloning to drive our design-build-test-learn cycle.

You will run Illumina MiSeq and NextSeq end-to-end, build large pooled libraries, and collaborate with enzyme engineering, chemical biology, and computational teams to translate sequencing data into actionable insights for platform decisions.

Qualifications

• 5+ years of laboratory experience in molecular biology and sequencing.
• Experience with Illumina MiSeq/NextSeq and NGS library prep.
• Hands-on Gibson and Golden Gate cloning workflows.
• Strong data quality, sample tracking, and documentation.
• Ability to collaborate in a fast-paced, cross-functional environment.

Responsibilities

• Perform NGS library preparation, QC, and end-to-end operation of Illumina platforms.
• Execute high-throughput molecular cloning workflows to build constructs and libraries.
• Assemble, quantify, and QC large pooled libraries ensuring coverage and diversity.
• Own sample management, barcoding, and data tracking in ELN/LIMS.
• Develop, optimize, and document scalable protocols for throughput and quality.
• Process and interpret raw sequencer output with computational colleagues.
• Collaborate with enzyme science, chemical biology, and ML teams.
• Maintain rigorous documentation and lab best practices; ensure safety.

Skills

NGS library prep

Illumina sequencing

Molecular cloning

Data analysis

Documentation/ELN/LIMS

Education

B.S. in Biology or related

M.S. in Biology or related

Tools

Illumina MiSeq

NextSeq 2000

ELN/LIMS

Job description

Senior Research Associate, Molecular Biology and Sequencing

Cambridge, MA USA

What if… you could pioneer a new approach to designing life’s most essential molecules?

FL116, backed by Flagship Pioneering, is an early-stage biotechnology company transforming the way biomolecules are synthesized. Our innovative platform has the potential to transform how critical research, diagnostic, and therapeutic molecules are manufactured. We are seeking passionate problem solvers ready to make a profound impact on biotechnology and therapeutic innovation.

Position Summary

Senior Research Associate – Molecular Biology & Sequencing

We are seeking a motivated, detail-oriented, and technically strong Sr. RA to join our Assay Development team. This role owns the next-generation sequencing and high-throughput cloning that generate the design-build-test-learn data powering our platform —

You will run Illumina MiSeq i100 and NextSeq 2000 instruments end to end, build and QC large pooled variant libraries, and partner closely with enzyme engineering, chemical biology, and computational colleagues to turn sequencing output into actionable insight.

This is an exciting opportunity to build and own core molecular biology capabilities within a fast-paced, collaborative startup. You are a hands-on experimentalist who thrives on rigorous execution, cares about data quality and sample provenance, and is eager to grow with a rapidly evolving technology platform.

Key Responsibilities

• Sequencing: Perform NGS library preparation, QC, and end-to-end operation of Illumina MiSeq i100 and NextSeq 2000 platforms, including run setup and troubleshooting
• Cloning: Execute high-throughput molecular cloning workflows (Gibson, Golden Gate, and related methods) to build constructs and variant libraries at scale
• Pooled library assembly and QC: Assemble, quantify, and quality-control large pooled variant libraries, ensuring coverage, diversity, and representation meet project requirements
• Sample management and tracking: Own sample management, barcoding, and data/metadata tracking across both sequencing and cloning workflows, maintaining accurate records in ELN/LIMS systems
• Develop, optimize, and document robust, scalable protocols; identify and implement opportunities for throughput, cost, and quality improvements
• Process and interpret raw sequencer output, working with computational colleagues to convert reads into actionable insights for platform and pipeline decisions
• Collaborate closely with cross-functional partners across enzyme science, chemical biology, and machine learning to ensure sequencing and cloning capabilities meet downstream needs
• Maintain rigorous experimental documentation, communicate results clearly, and contribute to knowledge sharing and lab best practices
• Comply with laboratory safety protocols and best practices in reagent, sample, and biohazard handling

Qualifications

• B.S. in Biology, Biochemistry, Molecular Biology, or a related discipline with 5+ years of relevant laboratory experience; M.S. with 3+ years.
• Extensive hands-on experience performing NGS library preparation, library QC, and sequencer operation on Illumina MiSeq and NextSeq platforms
• Hands-on experience performing Gibson, Golden Gate, and related molecular cloning workflows
• Demonstrated ability to generate high-quality, reproducible data with rigorous documentation and sample tracking
• Strong organizational skills and attention to detail, with the ability to manage multiple parallel workstreams
• Clear communicator who works effectively in fast-paced, collaborative laboratory environments

Preferred Qualifications

• Experience characterizing the products of nucleic acid modifying enzymes via sequencing and other analytical methods (LC-MS, HPLC, etc.)
• Experience converting raw sequencer output into actionable insights, including familiarity with demultiplexing, read QC, and basic analysis tooling (e.g., command line, Python, or R)
• Experience applying high-throughput cloning and NGS data to enzyme engineering projects
• Experience running high-throughput enzyme assays using basic lab automation (e.g., liquid handlers) and plate readers
• Experience constructing and testing large variant libraries through pooled functional testing (e.g., yeast surface display or a related method)
• Familiarity with electronic lab notebooks (ELNs), LIMS, or related data-management tools

Who You Are

• Innovative Pioneer: You are excited by the opportunity to explore new scientific frontiers and to build the molecular biology capabilities that unlock a novel synthesis platform.
• Collaborative Contributor: You work effectively across teams, communicate clearly, and value shared success in a highly interdisciplinary environment.
• Inventive Problem Solver: You approach challenges with curiosity and creativity, troubleshooting from first principles to develop elegant, reliable experimental solutions.
• Rigorous Operator: You take pride in clean data, careful sample provenance, and protocols others can trust and reproduce.
• Mission-Driven Individual: You are motivated by the opportunity to fundamentally change how biomolecules are synthesized and to impact human health and biotechnology.

More About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, generating billions in value. Flagship companies are known for addressing humanity’s most pressing challenges and advancing innovative solutions with global impact.

We are an equal opportunity employer and are dedicated to building diverse and inclusive teams. If you have some of the qualifications listed above but not all, we still encourage you to apply. We value passion, experience in many forms, and unique backgrounds.

Come pioneer the future with us.

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 $81,000 - $107,250. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL116 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL116'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 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].