ASPIRE Intern – Studio D3: Data-driven Models of Collective Cell Behavior

ASPIRE Intern – Studio D3: Data-driven Models of Collective Cell Behavior

The mission of the Allen Institute is to understand the principles that govern life and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.

The Allen Institute is searching for an ASPIRE Intern for its new Studio D3. Studio D3 develops and applies cutting-edge theoretical models, analytical frameworks, and scalable computational methods to extract principles that govern biology from multimodal biological data. The Allen Institute has collected and openly shared some of the largest datasets in life sciences. By integrating computation, data science, and quantitative modeling into the research ecosystem, Studio D3 helps drive discovery across diverse biological disciplines. 

The Studio D3 interns will be part of a cohort aimed at tackling problems of interest across biological areas, using methods from any of a variety of computational approaches from dynamical systems to machine learning and beyond.  The successful applicant will bring a strong computational background along with an interest in applying those skills to pressing biological questions. 

The intern will develop a data-driven biophysical modeling framework to infer the cell-to-cell interaction potential that governs collective cell behavior. Using pre-existing or new single-cell trajectories from microscopy timelapse data, we will develop a machine learning or Bayesian inference model that learns the fundamental force field (e.g., contact inhibition, long-range attraction) that best explains the observed cell movements. This quantitative platform will then be used to systematically characterize how these "interaction rules" are fundamentally altered when cells are subjected to different environmental conditions, moving beyond qualitative observation to a predictive, quantitative understanding of cell sociology. The successful applicant will be part of a cohort of interns dedicated to quantitative biological problems. 

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. 

We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment. 

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Applications must be received by January 12, 2026, to be considered.

Educational Objectives

• Learn about the biology of cell-to-cell interactions
• Learn about biological imaging data
• Learn about the application of modern machine learning to physical systems
• Develop machine learning methods for microscope images constrained by physical laws to help us gain insights about underlaying rules that govern the biological system
• Learn about a biological system and biological data
• Learn to read both computational methods and biology literature critically and incorporate findings into analysis
• Learn to write clean, reproducible and documented code in a collaborative setting using GitHub version control and code reviews
• Communicate progress and findings to relevant teams within the Allen Institute

Required Education and Experience

• Bachelor’s degree
• Demonstrated commitment to science
• This is a fully computational project requiring strong computational coding experience (computational science, machine learning, physics, applied math, or similar) and knowledge of physics
• The successful candidate will have strong skills in a form of quantitative scientific analysis such as dynamical systems, machine learning, data analysis, or similar

Work Environment 

• Open office environment

Position Type/Expected Hours of Work

• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with flexibility to work remotely on a limited basis.

Additional Eligibility Qualifications 

• Must have completed a Bachelor’s degree prior to the start of the program, and no earlier than December 1, 2023, and must not have an advanced degree in field relevant to the role/project
• Must be able to start in June or July 2026 and commit to the full one-year program, which will end on May 28, 2027
• Must be authorized to work in the U.S. for the program duration
• Must be 18 years of age or older

Additional Comments

• ASPIRE Interns are expected to participate as fully-engaged team members, attending and participating in team meetings, presenting on their work, etc.
• Aside from program activities, interns are expected to work full-time as regular team members unless otherwise approved by their manager
• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity requires U.S work authorization and does not sponsor work visas**

Annualized Salary

• $61,048 (non-negotiable)

Benefits

• ASPIRE Interns (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.