The Agmon Lab is focused on developing comprehensive, multi-scale models of cells – from their molecular underpinnings, to their integrated functions, to the organismic level with many heterogeneous cells interacting in a shared environment. Recent decades of biological research have generated abundant data on the composition, spatial organization, and dynamics of thousands of cell types; however, we need new tools that can transform this data into predictive models that can be used for scientific discovery. Rather than building isolated models that capture a narrow range of cellular behavior with a single class of representation, the next generation of computational models will combine multi-source and multi-level data with diverse, meaningful representations of biological mechanisms into integrative simulations. These simulations will be used to interpret the input datasets, make experimental predictions, identify medical solutions, and help us understand fundamental principles of biological organization.

The Agmon lab takes a 2-pronged approach to modeling whole cells: 1) develop computational methods and software for combining multi-omics datasets and diverse models into multi-scale simulations, and 2) apply these tools to build integrative simulations of whole microbiomes, which span molecular to multi-cellular scales.

Research keywords: computational systems biology, multi-scale modeling and simulation, cell biology, machine learning, complex adaptive systems

Accepting Lab Rotation Students: Fall Block 2024, Spring 1 and 2 Block 2025

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