Scientist I, Explanatory Modeling in the Continuum Space

The mission of Allen Institute for Cell Science is to develop a comprehensive and holistic approach to measure, describe, and model cell states and their dynamic changes over time. Our ultimate goal is to uncover the fundamental principles of multiscale, multicellular morphogenesis, including how groups of cells organize and achieve collective behaviors essential for life. Our approach encompasses multi-modal data collection including live 3D timelapse imaging, data analysis, theory, and predictions to understand cell states and cell state transitions in human induced pluripotent stem cell models. 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.

We are seeking a highly motivated and goal-oriented Scientist I - Explanatory Modeling in the Continuum Space, to development and implement multiscale models that explain how cellular events emerge from underlying processes given known physical and biological constraints. This role offers a unique opportunity to apply and integrate concepts of non-equilibrium statistical mechanics, stochastic processes and active matter to advance the field of cell science. Working with a team that includes computational biologists, simulation experts, quantitative and modeling scientists, and software engineers, this scientist will help build explanatory modeling frameworks that not only reproduce real cellular dynamics, but also predict the outcomes of experiments not yet conducted. This role will collaborate closely with the Institute’s technical and programmatic teams to achieve the Institute’s shared, programmatic objectives.

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.

Essential Functions

• Formulate and solve complex explanatory models involving stochastic processes, PDEs, and optimization in the continuum space
• Apply computational approaches to simulate and analyze biological systems and generate new insights
• Develop robust protocols and reproducible modeling frameworks to generate quantitative information from microscopy image data
• Use descriptive modeling and statistical analysis to interpret quantitative information to generate biological insights
• Develop and maintain custom scripts and software tools for image analysis, data processing, and modeling (Python proficiency required)
• Work closely with others in the institute to scale image and data analysis protocols into high throughput computation pipelines
• Coordinate with other programs in the Institute to ensure seamless integration and sharing of resources and data
• Maintain rigorous quality control standards and thorough documentation
• Work closely with other scientists to coordinate complex experiments
• Prepare written summaries and present activities internally and publicly
• Adherence to SOPs, GLPs and regulatory requirements

Required Education and Experience

• PhD in cell biology, biophysics, bioengineering or related science or engineering degree; or equivalent combination of degree and experience required

Preferred Education and Experience

• Proficiency with numerical algorithms for solving PDEs and optimization problems
• Deep knowledge of statistical mechanics concepts and their application to biological systems
• Extensive experience integrating neural networks into biophysical models to learn unknown parameters and capture complex interactions
• Strong understanding of biological processes, such as cell signaling, pattern formation, and gene regulation
• Ability to communicate complex concepts and connect them to biological problems
• Experience with 3D live-cell and timelapse imaging techniques and data analysis
• Advanced proficiency in Python programming
• Experience with developing or contributing to open-source tools/packages
• Familiarity with software engineering practices such as version management, build management and testing
• Excellent interpersonal skills
• 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

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

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

• $90,000 - $112,400*

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

Employees (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