Senior Research Associate, Molecular Biology and Sequencing

flagshippioneeringinc; Cambridge; On-site; GBP 50,000 - 70,000; Full time

Job summary

Flagship Pioneering in Cambridge seeks a Senior Research Associate to advance molecular biology capabilities for sequencing and cloning within a fast-paced startup environment.

You will run Illumina MiSeq i100 and NextSeq 2000, build large pooled variant libraries, and ensure data provenance in ELN/LIMS while collaborating across enzyme science, chemical biology, and machine learning to turn sequencing reads into actionable platform insights.

Qualifications

• BS/MS degree with 3+ years (MS) or 5+ years (BS) in biology-related labs.
• Extensive hands-on NGS library prep, QC, and sequencing on MiSeq/NextSeq platforms.
• Hands-on molecular cloning workflows (Gibson, Golden Gate) and variant library handling.
• Demonstrated ability to generate high-quality data with rigorous documentation and sample tracking.
• Strong organizational skills and effective communication in fast-paced lab environments.

Responsibilities

• Perform NGS library preparation, QC, and end-to-end sequencing on Illumina platforms.
• Execute high-throughput cloning workflows to build constructs and libraries at scale.
• Assemble and QC large pooled libraries ensuring coverage and representation.
• Manage samples, barcoding, and data/metadata in ELN/LIMS systems.
• Develop, optimize, and document scalable protocols for throughput and quality.
• Interpret raw sequencing data with computational colleagues to guide platform decisions.
• Collaborate with enzyme science, chemical biology, and ML teams to meet downstream needs.
• Maintain rigorous experimental documentation and lab safety practices.

Skills

NGS library prep

Illumina sequencing

Gibson assembly

Golden Gate

Data tracking

Cross-functional collaboration

Education

B.S. in Biology or related

M.S. preferred

Tools

Illumina MiSeq

NextSeq 2000

ELN/LIMS

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: