Scientist, Computational Vaccine Design

Position Summary

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.

Key Responsibilities

• Use high-dimensional datasets (e.g., mutational scanning, 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

Basic Qualifications

• 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
• Experience or training in antigen design leveraging vaccine immune response readouts
• 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

Preferred Qualifications

• Experience in vaccine design
• 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)

About Flagship

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 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. 

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.

The salary range for this role is $115,000 - $165,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Apriori Bio, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Apriori Bio, Inc.'s good faith estimate as of the date of publication and may be modified in the future.