The E. coli whole-cell modeling project : growth rate control and environmental responses
Abstract/Contents
- Abstract
- Whole-cell modeling is an approach to building fine-grained computational models that accounts for every molecule and the known mechanisms and interactions of gene products in a cell. The E. coli Whole-Cell Modeling Project applies this approach to the model organism E. coli by integrating data and mechanistic understanding of E. coli generated by many labs and has the potential to lead to rapid biological discovery while providing a means of assessing the body of work representing our collective understanding of E. coli physiology. Creating a model of this scale can provide deep biological insights into complex regulatory networks and growth control, identify inconsistencies between datasets used to construct the model, demonstrate emergent behavior to suggest novel behavior arising from complex interactions, and make biological predictions that have been experimentally validated. Growth and environmental responses are essential for living organisms like bacteria to survive and adapt to constantly changing environments and the model can also be used to better understand these processes. With the inclusion of regulation and kinetics rates, the E. coli model exhibits a mechanistic growth rate that is dependent on the environment and internal simulation state and no longer confined to environmental growth conditions used to parameterize the model. Importantly, the model also demonstrates more appropriate responses to environmental limitations and shifts and provides a means to assess the factors that control growth rate in the context of the entire cell. This sets a critical foundation for expanding the model to new environmental conditions and allows for additional predictive capabilities.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2022; ©2022 |
| Publication date | 2022; 2022 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Ahn-Horst, Travis Andrew |
|---|---|
| Degree supervisor | Covert, Markus |
| Thesis advisor | Covert, Markus |
| Thesis advisor | Bintu, Lacramioara |
| Thesis advisor | Spakowitz, Andrew James |
| Degree committee member | Bintu, Lacramioara |
| Degree committee member | Spakowitz, Andrew James |
| Associated with | Stanford University, Department of Bioengineering |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Travis Ahn-Horst. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/kw189wh6131 |
Access conditions
- Copyright
- © 2022 by Travis Andrew Ahn-Horst
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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