Job Openings at the Allen Institute

Are you ready for new challenges and new opportunities? Join our team in Seattle!
Current job opportunities are posted here as they become available.



Scientist I, Quantitative Cell Biologist in Agent-based Modeling

Department: Animated Cell

Scientist I, Quantitative Cell Biologist in Agent-based Modeling

The mission of the Allen Institute for Cell Science is to create multi-scale visual models of cell organization, dynamics, and activities. Our approach encompasses large scale data collection, observation, theory, and predictions to understand cellular behavior in normal and pathological contexts. As a division within the Allen Institute, the Allen Institute for Cell Science uses a team-oriented approach, focusing on accelerating foundational research, developing standards and models, and cultivating new ideas to make a transformational impact on science.

To learn more, please explore our website at

The Allen Institute for Cell Science seeks a talented and passionate individual to join our team as a Quantitative Cell Biologist specialized in agent-based modeling. This position offers a unique dual focus that will enable us to uncover and study underlying rule-based mechanisms that drive emergent multi-scale cell organization and dynamics: first, to develop agent-based models; and second, to iterate on these models with both in silico and laboratory experiments and analyses. This multidisciplinary position will require an extensive knowledge of cellular and molecular biology along with experience in integrating computational models with experimental results to produce new testable hypotheses. The hire may also be required to supervise the activities of others as they will work primarily in cross-team projects with other agent-based modelers, spatial modelers, engineers, and computational and experimental cell biologists to achieve the Institute’s goals.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

The ideal candidate for this role will:

  • Have a broad expertise in cell/molecular biology, image analysis, and spatial modeling of dynamic emergent systems
  • Be skilled at programming to solve problems efficiently and robustly
  • Be curious and enjoy learning new tools, techniques, and technologies, while also enjoying iterating on experiments and software to polish their work
  • Be skilled at interfacing across multiple groups and stakeholders who have different types of expertise
  • Be adept at collecting data and designing experiments with the ability to define problems, collect data, establish facts, and draw valid conclusions

Essential Functions:

  • Collaboratively design and develop robust, reproducible, and extensible agent-based and/or spatial models that can be compared to quantitative experiments/descriptions of cell organization, dynamics, activities, and functions
  • Establish, test, and iterate on hypotheses, rules and parameters that drive these models to uncover and test likely mechanisms that drive emergent multi-scale organization and dynamics
  • Rapidly develop preliminary models for rapid experiment-to-model iterative prototyping/sandboxing
  • Collaborate with image and data analysis experts across multiple teams to perform analyses on the models
  • Collaborate with other teams in the institute to combine and scale-up model/image/data analysis protocols towards a vision of a high throughput computation pipeline with integrated models
  • Coordinate with other programs in the Institute to ensure seamless integration and sharing of resources and data
  • Prepare written and visual summaries and present activities internally and publicly

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education & Experience

  • PhD in a biological science (e.g., cell biology, biophysics, bioengineering), related science or engineering field, or equivalent combination of degree and experience

Preferred Education & Experience

  • Extensive knowledge, background, and expertise in quantitative biological science
  • Extensive experience developing, applying, and analyzing agent-based spatial models of biological systems
  • Some experience in data and/or image analysis of cell biological microscope image data
  • Excellent interpersonal skills
  • Knowledge, background, and expertise in quantitative cell biology
  • Experience modeling biological systems at the organelle level of the mesoscale, i.e., 0.1µm—10µm
  • Experience using more than one computer language, e.g., Python, C++, Java
  • Experience with Python/Jupyter notebooks
  • Published articles describing agent-based models or methods
  • Experience in 3D image processing and segmentation
  • Experience in 3D live-cell and time-lapse imaging techniques and data analysis
  • Experience with modern machine learning approaches
  • Experience in a range of state-of-the-art light microscope modalities (especially 3D confocal and spinning disk microscopes)
  • Experience with developing or contributing to open-source tools/packages
  • Experience utilizing software engineering practices such as version control, build management, and test-driven development, documentation, and collaborative code development
  • Experience working in a multi-disciplinary environment in academic or industrial settings
  • Ability to work both independently and in a collaborative, multi-disciplinary environment
  • Careful attention to detail
  • Experience with cloud computing

Work Environment

  • May enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type/Expected Hours of Work

  • This role is currently working onsite and remotely when possible, due to COVID-19 and our focus on employee safety. We continue to evaluate the safest options for our employees.


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.





Applicant Tracking System Powered by ClearCompany HRM Applicant Tracking System