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Why build whole-cell models?
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  1. WholeCellViz: data visualization for whole-cell models
    Personal Author:
    Lee, Ruby; Karr, Jonathan R; Covert, Markus W;
    Published:
    Aug 21 2013
    Source:
    BMC Bioinformatics. 2013; 14:253.
    Description:
    Background : Whole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and analyzing complex, high-dim...
    File Type:
    Filetype[PDF - 1.84 MB]
  2. WholeCellKB: model organism databases for comprehensive whole-cell models
    Personal Author:
    Karr, Jonathan R.; Sanghvi, Jayodita C.; Macklin, Derek N.; Arora, Abhishek; Covert, Markus W.;
    Published:
    Nov 21 2012
    Source:
    Nucleic Acids Res. 2012; 41(Database issue):D787-D792.
    Description:
    Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors. Whole-cell model development requires comprehensive model organism databases. WholeCellKB (http://wholecellkb.stanford.edu) is an open-source web-based soft...
    File Type:
    Filetype[PDF - 2.49 MB]
  3. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
    Personal Author:
    Karr, Jonathan R.; Williams, Alex H.; Zucker, Jeremy D.; Raue, Andreas; Steiert, Bernhard; Timmer, Jens; Kreutz, Clemens; Wilkinson, Simon; Allgood, Brandon A.; Bot, Brian M.; Hoff, Bruce R.; Kellen, Michael R.; Covert, Markus W.; Stolovitzky, Gustavo A.; Meyer, Pablo;
    Corporate Author:
    DREAM8 Parameter Estimation Challenge Consortium
    Published:
    May 28 2015
    Source:
    PLoS Comput Biol. 2015; 11(5).
    Description:
    Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which...
    File Type:
    Filetype[PDF - 1.02 MB]
  4. The Future of Whole-Cell Modeling
    Personal Author:
    Macklin, Derek N.; Ruggero, Nicholas A.; Covert, Markus W.;
    Published:
    Feb 17 2014
    Source:
    Curr Opin Biotechnol. 2014; 28:111-115.
    Description:
    Integrated whole-cell modeling is poised to make a dramatic impact on molecular and systems biology, bioengineering, and medicine--once certain obstacles are overcome. From our group's experience building a whole-cell model of Mycoplasma genitalium, ...
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    Filetype[PDF - 333.93 KB]
  5. Accelerated discovery via a whole-cell model
    Personal Author:
    Sanghvi, Jayodita C.; Regot, Sergi; Carrasco, Silvia; Karr, Jonathan R.; Gutschow, Miriam V.; Bolival, Benjamin; Covert, Markus W.;
    Published:
    Nov 03 2013
    Source:
    Nat Methods. 10(12):1192-1195.
    Description:
    To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies be...
    File Type:
    Filetype[PDF - 1014.87 KB]