Title: Model-driven discovery through a whole-cell computational model of Escherichia coli

Abstract: Throughout many scientific and engineering disciplines, mathematical models have been pivotal in helping scientists and engineers better understand complicated systems, develop hypotheses, predict behaviors, and make model-guided discoveries. The E. coli whole-cell modeling project aims to bring this approach into biology by constructing a detailed mathematical representation of the most well-characterized system in biology — the E. coli cell. The whole-cell model is composed of multiple, smaller submodels that each represent a particular biological process within an E. coli cell, which are then integrated into a larger model that can simulate the growth of the entire cell under multiple environments. In total, the model incorporates more than 19,000 heterogeneous parameters gathered from decades of research performed on this model organism. The whole-cell modeling team within the Covert Lab has been leading this project for more than ten years.

In my Ph.D. defense, I will first describe how the E. coli whole-cell model was built and our general strategy for using the model in model-driven discovery. Next, I will share my efforts in building data pipelines between the whole-cell model and EcoCyc, the largest online database for E. coli, to streamline the curation of model parameters and broadly share the model outputs to the scientific community. Lastly, I will present how the whole-cell model was updated to account for E. coli's transcription unit structures, and highlight the discoveries I made during this process.

Please contact Madelyn Bernstein for the Zoom link