Senior Research Associate, Molecular Biology and Sequencing

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

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

A broad range of other benefits

Job summary

Flagship Pioneering, Inc. is seeking a Senior Research Associate for Molecular Biology & Sequencing to drive next-gen sequencing and high-throughput cloning within a fast-paced startup.

You will run Illumina MiSeq and NextSeq end-to-end, build variant libraries, and partner with engineers and computational scientists to translate reads into actionable insights. You are an hands-on experimentalist focused on data quality, sample provenance, and scalable protocols, eager to grow with a rapidly

Qualifications

• B.S. in Biology or related field; M.S. preferred, with 3+ years lab experience.
• Extensive experience in NGS library prep, QC, and Illumina platforms.
• Hands-on Gibson and Golden Gate cloning workflows.
• Strong data quality, documentation, and sample-tracking.
• Ability to collaborate across enzyme science and computational teams.

Responsibilities

• Perform NGS library preparation and end-to-end operation of Illumina MiSeq i100 and NextSeq 2000.
• Execute high-throughput molecular cloning workflows (Gibson, Golden Gate) to build constructs and variant libraries.
• Assemble, quantify, and QC large pooled variant libraries with adequate coverage and representation.
• Own sample management, barcoding, and data tracking across sequencing and cloning workflows
• Develop, optimize, and document robust, scalable protocols for throughput, cost, and quality.
• Process raw sequencer output and work with computational colleagues to derive actionable insights.
• Collaborate with cross-functional partners in enzyme science, chemical biology, and ML to meet downstream needs.
• Maintain rigorous experimental documentation and lab safety practices.

Skills

Molecular biology

NGS library prep

Sequencing data analysis

Data documentation

Sample management

Education

B.S. in Biology or related

M.S. in Biology or related

Tools

Illumina MiSeq

NextSeq 2000

ELN/LIMS

Python

R

Job description

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.

Compensation and Benefits

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.

• healthcare coverage
• annual incentive program
• retirement benefits
• 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.