Scientist , Explanatory Modeling Continuum Space

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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 develop 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…