Senior Research Associate, Molecular Biology and Sequencing

Flagship Pioneering•Cambridge, MA

About The Position

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. 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.

Requirements

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

Nice To Haves

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

Responsibilities

Perform NGS library preparation, QC, and end-to-end operation of Illumina MiSeq i100 and NextSeq 2000 platforms, including run setup and troubleshooting
Execute high-throughput molecular cloning workflows (Gibson, Golden Gate, and related methods) to build constructs and variant libraries at scale
Assemble, quantify, and quality-control large pooled variant libraries, ensuring coverage, diversity, and representation meet project requirements
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