Senior Scientist, Molecular Biology

Flagship Pioneering, Inc.•Cambridge, MA

About The Position

Serif Biomedicines, Inc. is a privately held, early-stage biotechnology company developing a novel approach to gene therapy that can address currently untreatable diseases. Serif Biomedicines was founded by Flagship Pioneering, an innovation enterprise that conceives, creates, resources, and grows first-in-category life sciences companies. Flagship Pioneering has created over 100 groundbreaking companies over the past twenty years, all of which are pioneering novel and proprietary biological, industrial, and engineering approaches to solve major needs in human health and sustainability. These companies include Moderna (MRNA), Syros Pharmaceuticals (SYRS), Seres Therapeutics (NASDAQ:MCRB), Generate Biomedicines, Tessera Tx, Evelo Biosciences (EVLO), and Indigo Agriculture. We are seeking a highly innovative and driven Senior Scientist, Molecular Biology to lead the design and generation of next-generation DNA constructs enabling programmable medicines. This role is ideal for a scientist who thrives at the intersection of synthetic biology, high-throughput cloning, and computational sequence engineering. You will play a critical role in building scalable platforms for plasmid DNA design, construction, and optimization, leveraging automation, algorithm-driven sequence design, and data-centric workflows. The ideal candidate brings deep technical expertise, creative problem-solving, and a passion for pushing the boundaries of nucleic acid engineering in a fast-paced, entrepreneurial environment. The Senior Scientist will report to the Director of Molecular Biology and is expected to manage a direct report. The role involves close collaboration with other Scientists and group leads across the company as part of a highly collaborative and growing R&D group.

Requirements

PhD with 5+ years of relevant experience in relevant scientific discipline (Molecular Biology, Synthetic Biology, Bioengineering).
Deep expertise in molecular cloning, plasmid design, DNA construct engineering, and E. coli strain engineering, including genetic modification and expression system development.
Demonstrated experience with automated sequence design tools, scripting (e.g., Python), and/or computational biology workflows.
Strong background in high-throughput and scalable molecular biology techniques.
Experience with NGS data analysis and sequence validation pipelines.
Proven ability to lead complex projects and influence cross-functional teams.
Strong mentorship skills with commitment to developing others. Previous technical or professional management experience.
Excellent communication skills, with the ability to translate complex ideas across disciplines.

Nice To Haves

Familiarity with lab automation platforms and workflow integration is a plus.

Responsibilities

Lead the end-to-end design and construction of plasmid DNA constructs, including vector architecture, gene synthesis strategies, and high-efficiency cloning workflows (e.g., Gibson, Golden Gate, recombination-based methods).
Drive automated and computational sequence design, utilizing advanced tools and pipelines for codon optimization, regulatory element tuning, and multi-parameter construct optimization.
Establish vendor relationships with an emphasis on hybrid internal and external capabilities to remain agile while minimizing the impact on project timelines.
Develop and implement variable-throughput cloning and screening platforms, standardized workflows, and scalable molecular biology processes.
Own sequence analysis pipelines, variant analysis, and construct QC.
Collaborate cross-functionally with diverse teams in the company. The ideal candidate will have a direct relationship with CMC. The chosen candidate will provide designs, material and timelines to CMC, as requested.
Mentor and guide junior scientists, establishing best practices in molecular biology, experimental design, and data rigor.
Establish a rigorous ELN environment including sample management, version-controlled sequence design, and reproducible research practices.
Communicate scientific insights effectively, presenting results across functional teams and leadership to drive strategic decision-making.