Senior Research Associate, Molecular Biology and Sequencing

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 assa