Apriori Bio, Inc Cambridge, MA Scientist, Computational Vaccine Design

We are seeking a Scientist to join a dynamic team applying computational and data-driven approaches to design novel antigens and evaluate vaccine responses. At Apriori Bio, we have built our biology-enabled AI/ML platform Octavia™ to map viral fitness landscapes, predict immune escape trajectories, and design vaccines to elicit an optimal protective response to future challenges. The successful candidate will contribute to the development and application of computational methods—including structural modeling, machine learning, and statistical inference— that build on Octavia™ insights to support the company’s vaccine design efforts.

Experience working with protein engineering and immunological datasets is valuable, as is interest or training in high-throughput functional genomics, virology, or vaccinology.

The Scientist will work closely with both computational and experimental colleagues to interpret results, generate hypotheses, and support antigen design. This role is ideal for scientists eager for a unique opportunity to learn and innovate within an interdisciplinary, fast-paced startup environment.

• Use high-dimensional datasets (e.g., mutational scrolling, NGS-based phenotypic screens) and computational approaches—including structural modeling, sequence analysis, and machine learning—to support antigen and immunogen engineering
• Apply and refine computational models that integrate screening data with structural and sequence-based features to guide biomolecule engineering
• Generate hypotheses and design analyses that inform evaluation of novel immunization strategies (in partnership with experimental teams)
• Identify, evaluate, and curate external datasets relevant to vaccine design and antigen optimization
• Develop reproducible computational tools and pipelines for data-driven product design that can be integrated into broader platform workflows
• Collaborate with engineers, computational scientists, and experimentalists to execute project goals and ensure smooth integration of computational findings
• Work with immunology and characterization teams to interpret vaccine immunogenicity using next-generation immune monitoring and antibody profiling tools
• Clearly communicate results and insights to colleagues across scientific and cross-functional teams
• Tackle difficult scientific problems with creativity and resilience while iterating quickly as new data emerges
• Take ownership of complex, open-ended scientific questions, driving analyses forward through ambiguity while balancing speed, rigor, and collaborative problem-solving

• Ph.D. in bioengineering, immunology, computational biology, or a related field (or equivalent research experience)
• Experience applying data-driven protein engineering methods to predict and affect protein function, including structural and sequence-based machine-learning approaches
• Solid statistical and quantitative foundation, with the ability to translate complex biological datasets into actionable insights
• Strong scientific programming skills (Python preferred) and familiarity with best practices in reproducible scientific computing
• Experience working with high-throughput biological data or NGS-based assays, including modeling and statistical analysis
• Experience using version control and collaborative coding workflows

• Experience with deep learning approaches
• Exposure to antibody characterization, immune profiling, or immune repertoire analyses
• Experience with NGS data pipelines, from processing to interpretation
• Familiarity with cloud or distributed computing environments
• Familiarity with storage, analysis and transformation of large tabular datasets and relational databases
• Laboratory experience in molecular biology, biochemistry, or immunology (a plus, not required)

Flagship Pioneering is a biotechnology 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…