Back to Jobs

Data Scientist

Flagship Pioneering
Cambridge, MA
About the Role

At Apriori Bio, we have built our unique technology platform Octavia to help survey viral landscapes and improve vaccine design towards increased efficacy and breadth. This role will serve as a critical part of this effort, sitting on the Platform team that develops and builds the key capabilities supporting Octavia. You will partner with our wet-lab scientists as well as our broader computational team to turn our high-throughput immune landscaping data into actionable insights and features for the design of better vaccine candidates. Additionally, you will develop innovative approaches predicting the ability of antigens to evade existing immunity, thus enabling the design of the next generation of variant-resilient vaccines. In this cross-functional role, you will have the opportunity to utilize our in-house and external databases, generate data-driven insights, and contribute to the expansion and refinement of Octavia.

Position Summary

Apriori Bio is seeking a Data Scientist with a track record of developing and successfully applying analytical tools to high-throughput sequencing assays. This role is positioned at the interface between the high-throughput biological readouts that power Octavia and the expanding set of platform capabilities enabling the design of better vaccine candidates against infectious disease. Experience in the analysis and interpretation of high-throughput functional and/or genomic assays (e.g. deep mutational scanning, barcode-based NGS assays, and other library based phenotypic assays) is desired. The role requires strong data visualization and communication skills, as well as a proficency in bioinformatics. Technical expertise in protein engineering or structure, virology, vaccinology, viral phylogenetics and/or viral phylodynamics is preferable. This individual will join a dynamic, rapidly growing and collaborative team, and should also be comfortable in a fast-paced start-up environment.  

Core Responsibilities:

  • Execute and manage high-throughput sequencing analysis pipelines
  • Analyze and interpret results of high-throughput experiments, assessing relevance for associated programs and communicating evaluated results to program teams.
  • Collaborate with wet-lab scientists to design experiments for assay development, program advancement, & expansion of the Octavia platform.
  • Collaborate with broader Apriori team to develop and optimize new high-throughput assays to expand the capabilities & impact of Octavia
  • Perform longitudinal data analyses to support experimental decision-making & platform development.
  • Integrate various data sources to engineer useful features for predictive modeling & antigen design.
  • Assist with organizing, extracting, and uploading proprietary experimental information programmatically with Benchling ELN’s SDK.
  • Create clear, user-friendly visualizations to be developed into dashboards and automated workflows.
  • Regularly present platform progress in research and executive team meetings, creating comprehensive reports and slides for widespread communication.
  • Uphold data management integrity and reproducibility through established software engineering best practices.
  • Monitor cutting-edge technologies and models and identify potential collaboration opportunities across the Flagship Ecosystem.

Qualifications and Skills:

  • Ph.D. in life sciences or a quantitative field.
  • Proficiency in writing production-standard Python code, especially with packages in the scientific computing ecosystem (NumPy, SciPy, Matplotlib, pandas, etc.).
  • Experience with analyzing and interpreting high-throughput experimental data
  • Solid bioinformatics background with proficiency handling and analyzing sequence data
  • Strong scientific and quantitative acumen, with a demonstrated ability to integrate this acumen into platform & model building
  • Familiarity with collaborative coding using GitLab best practices and commands.
  • General proficiency with cloud platforms, specifically AWS.
  • Demonstrable extensive experience or study in statistical/quantitative modeling & machine learning.
  • Working knowledge of quantitative data pipelines, including workflow orchestration, ETL processes, quality control management, and reporting.
  • Knowledge in at least one ML framework (PyTorch/TensorFlow/Jax).
  • Effective working in fast-paced, highly collaborative, and matrixed teams.
  • Exceptional communication skills, especially with requirements gathering and data presentation.

Preferred Additional Skills:

  • Familiarity with immunology, vaccinology, or infectious disease concepts.
  • Previous experience in a biotech startup.
  • Experience building technology to process high-throughput sequencing (HTS) assays, preferably display-based HTS systems like phage, yeast, and/or mammalian cell surface display.
  • Hands-on experience with Databricks, including cluster management, Unity Catalog–based data workflows, Spark/PySpark, and developing SQL queries/dashboards.
  • Knowledge of anomaly detection methods, structural biology visualizations, and data modeling.
  • Familiarity with cloud native tools such as AWS s3 and ec2.
  • Understanding of DevOps, change management, and technical documentation concepts.
  • Ability to communicate effectively across various platforms, such as Jupyter notebooks, PowerPoint, Teams, and verbal discussions.

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

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.
Posted 2026-01-09

Recommended Jobs

Clinical Sales Manager - Boston, MA to Hartford, CT

Boston, MA

Abbott is a global healthcare leader that helps people live more fully at all stages of life. Our portfolio of life-changing technologies spans the spectrum of healthcare, with leading businesses and…

View Details
Posted 2025-12-08

Home Worker for senior care - Entry Level Opportunity

Guardian Angel Senior Services
Marlborough, MA

GUARDIAN ANGEL SENIOR SERVICES are actively Hiring caregivers to support elderly clients to make a difference in their life & help them in their daily livings. No prior experience required — w…

View Details
Posted 2026-01-05

Associate Director, US Omnichannel & Digital Strategy

Galderma
Boston, MA

Galderma is the emerging pure-play dermatology category leader, present in approximately 90 countries. We deliver an innovative, science-based portfolio of premium flagship brands and services that sp…

View Details
Posted 2025-12-24

Security Engineer 4

Oracle
Boston, MA

Job Description Responsible for the planning, design and build of security architectures; oversees the implementation of network and computer security and ensures compliance with corporate secu…

View Details
Posted 2026-01-10

Administrative Director (Leadership) - RN

Pittsfield, MA

Title:Administrative Director (Leadership) – RN Location:Pittsfield, MA (On-Site) Facility: Berkshire Medical Center – Berkshire Health Systems Inc Duration & Type:13 Week Contract Shift:Days | Sh…

View Details
Posted 2026-01-10

Senior Scientist, Process Development (Watertown, MA)

CEDENT
Watertown, MA

We are seeking a highly motivated and team-oriented professional with entrepreneurial spirit to join our company! This is an exciting opportunity for a well-qualified candidate to join a rapidly growi…

View Details
Posted 2025-12-08

Laborer - (Hospital Housekeeper)

Cambridge Health Alliance
Cambridge, MA

Requisition Number: 662 Pay Range: $16.98 - $28.28 per hour Location: CHA Cambridge Hospital  Work Days: 10:00 PM - 6:00 AM Weekends   Category: Service and Trade   Department: Environmental Se…

View Details
Posted 2025-11-27

Car Wash District Manager

Prestige Capital Group
Worcester, MA

Car Wash District Manager Locations: Worcester Area - Main Office is in Canton MA  Position Type: Full-Time, In-Person Compensation: $80,000+ annually Position Overview We are seeking…

View Details
Posted 2026-01-01

Senior Site Reliability Engineer (SRE)

Americas Test Kitchen
Boston, MA

America's Test Kitchen (ATK) is seeking a Senior Site Reliability Engineer (SRE) to focus on the stability, scalability, and performance of our core Cloud Infrastructure and Database Systems. This hig…

View Details
Posted 2025-12-10

Copywriter

Unreal Snacks
Boston, MA

About Unreal We're on a mission to unjunk the world, starting with our favorite food group: CHOCOLATE. Our story began when two kids who loved candy got tired of being told they couldn't eat it…

View Details
Posted 2026-01-09