Mike's Notes
An early talk by Markus Covert.
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Last Updated
11/05/2025
A Computational Whole-Cell Model Predicts Genotype From Phenotype
A 2013 talk by Markus Covert at the Qualcomm Institute.
Abstract: Francis Crick first called for a coordinated worldwide scientific effort to determine a "complete solution" of the bacterium Escherichia coli. We have been working for some years now to complete a model of E. coli that takes into account all of the known functions of every well-annotated gene, in order to better understand and predict the behavior of this scientifically-relevant and industrially-significant model organism. I will discuss our ongoing efforts to improve this model, most recently with new modeling added to better describe growth rate control, transcription unit architecture and tRNA metabolism. I will then highlight our newest "whole-colony" models, a multi-scale modeling effort in which every individual within a simulated colony is running the latest version of the whole-cell model, to calculate population-level emergent behaviors based on molecular interactions and events as the colony responds to the sudden introduction of antibiotics.
This is a part of a series of seminars organised by the Theory of Living Systems (Australia and NZ). The host is Michael Stumpf a professor of theoretical systems biology in the School of BioSciences and School of Mathematics and Statistics at The University of Melbourne. His research focuses on using mathematical, statistical and computational methods to understand how cells make decisions, and how we can influence their decisions.
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