Sr. Scientist, Strain Engineering

About Invaio Sciences

Invaio Sciences, founded by Flagship Pioneering, is a bio platform company accelerating the leap to nature-positive agriculture. The company builds on advances in human health and digital innovation to develop biological technologies for crop health, enabling farmers to both improve yields and use more natural crop health solutions.

About the role

Our Research & Development team based in Cambridge, MA is seeking a highly motivated and skilled Senior Scientist or Engineer to drive the design, construction, and optimization of engineered microbial strains (Pichia, Bacillus, Aspergillus) in support of our proprietary microbial technologies for agricultural applications. 

This is an on-site, hands-on bench role with a strong emphasis on molecular biology, genome engineering, pathway optimization, and high-throughput strain screening. You will work closely with fermentation, analytics, and bioassay teams to translate engineered strains into robust, scalable production systems. This role is ideal for a scientist who enjoys deep technical ownership at the bench and solving complex biological engineering problems. 

What you'll do

 Strain Engineering & Expression Development 

• Design, construct, and optimize engineered microbial strains for peptide and protein expression 
• Execute molecular biology workflows to generate single- and multi-gene constructs 
• Support strain optimization through iterative build–test–learn cycles 
• Develop and implement screening strategies to evaluate expression performance across strain variants 

Expression Analysis & Assay Development 

• Develop, adapt, and execute analytical assays to assess expression levels, product quality, and stability 
• Establish scalable screening workflows to enable comparison of large numbers of engineered strains 
• Analyze and interpret expression data to guide strain selection and optimization 

Peptide & Protein Purification 

• Develop and optimize peptide and protein purification strategies appropriate for early-stage screening and characterization 
• Execute purification workflows using chromatographic and non-chromatographic techniques 
• Optimize purification conditions to improve yield, purity, and reproducibility 
• Collaborate with process development and analytical teams to transition purification approaches as projects mature 

Team & Cross-Functional Collaboration 

• Mentor and lead a team of young scientists 
• Partner with fermentation, analytics, and bioassay teams to ensure strain outputs meet downstream needs 
• Generate material to support in vitro assays, greenhouse studies, and field trials 
• Contribute to project planning, data reviews, and technical decision-making 

Scientific Rigor & Documentation 

• Design experiments, analyze data, and document results in electronic laboratory notebooks 

• Prepare technical reports, protocols, and presentations for internal stakeholders 
• Contribute to invention disclosures and intellectual property development 
• Uphold high standards of data quality, reproducibility, and laboratory best practices 

Qualifications & Experience

• Ph.D. in Microbiology, Molecular Biology, Biochemical Engineering, Synthetic Biology, or related discipline 
• 3+ years of relevant laboratory experience in an industry setting 
• Strain Engineering & Molecular Biology Extensive experience in molecular cloning and genetic engineering 
• • Experience constructing and evaluating engineered strains for recombinant expression 
  • Ability to troubleshoot expression challenges through experimental iteration 
• Screening & Analytical Assays
• • Experience developing and running expression screening assays
  • Familiarity with protein/peptide quantification and characterization methods 

• • Strong data analysis and interpretation skills 
• Purification & Bioprocessing
• • Hands-on experience with pepti