Senior Scientist, NGS and Molecular Biology

Company Summary:

Founded by Flagship Pioneering in 2021, Metaphore aims to unlock breakthroughs that outperform today’s drugs for maximum patient impact, We adapted this idea to drug discovery. MIMIC™, our computationally driven bioplatform that couples machine learning with molecular mimicry, engineers therapeutics to trigger a desired biological response. Our MIMIC platform opens the possibility to develop engineered medicines with specific features to access a range of targets, including those that were previously intractable. Flagship and Metaphore have also just announced a $600M research collaboration with Novo Nordisk to develop up to two next-generation therapeutics for obesity management.

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Position Summary:

Metaphore is seeking a highly motivated, collaborative, and detail-oriented Senior Scientist with expertise in recombinant DNA technologies, vector design, and phage/yeast/mammalian display systems. In this role, you will lead the design and generation of plasmid constructs, antibody/protein libraries, and molecular display platforms to advance therapeutic discovery efforts. The ideal candidate will thrive in a fast-paced, collaborative biotech environment and have experience with automation, high-throughput screening, and cloning.

Key Responsibilities:

Vector Design & Molecular Cloning

• Design and construct expression vectors (plasmid/viral) for gene expression, knockdown, and editing.
• Apply traditional and high-throughput cloning techniques (e.g., Gibson Assembly, Golden Gate, Gateway).
• Manage construct inventories using LIMS platforms (e.g., Benchling).

Display Library Engineering

• Engineer phage, yeast, and mammalian display libraries (e.g., scFv, Fab, sdAb, and other related nanobodies).
• Develop and execute biopanning and affinity maturation strategies.
• Implement technologies such as deep mutational scanning (DMS) and massively parallel reporter assays (MPRA) to generate data for company machine learning driven platform.
• Comfortable analyzing data using Python, R, and Linux-based bioinformatics tools.

High-Throughput & Automation

• Collaborate with automation engineers, protein sciences, research informatics, and discovery to implement scalable workflows for high-throughput molecular cloning and screening.

Experimental Design & Collaboration

• Partner cross-functionally with protein engineering, bioinformatics, and screening teams to advise on experimental strategies and DNA designs to enable function-first screening.
• Rigorously document protocols, results, and quality control metrics.
• Drive innovation in molecular and cellular platform development.

Qualifications:

• PhD in Molecular Biology, Biochemistry, Biophysics, or related field with 5+ years of relevant experience
• Expertise in:
  • Molecular cloning and vector engineering
  • Display platforms (phage, yeast, ribosome, mammalian)
  • Protein engineering and affinity maturation
• Strong working knowledge of:
  • Geneious Prime, SnapGene, Benchling, Orchestra
  • Python/R for data analysis
  • Automation systems and high-throughput workflows
  • Engaging and managing CROs

This is an exciting opportunity to work on cutting-edge therapeutic discovery with a multidisciplinary team. You'll help shape the future of our molecular design and discovery engine while contributing to impactful scientific innovation.

Values and Behaviors

• We are seeking individuals with an entrepreneurial spirit, agility and strong communication skills, comfort working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidate.
• At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies

Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates.  The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team.   Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.