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Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

CITE Title : Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models Personal Author(s) : 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 Authors(s) : DREAM8 Parameter Estimation Challenge Consortium Published Date : May 28 2015 Source : PLoS Comput Biol. 2015; 11(5). URL : https://stacks.cdc.gov/view/cdc/31978 Karr, Jonathan R. et al. (2015). Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. 11(5). Karr, Jonathan R. et al. "Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models" 11, no. 5 (2015) Karr, Jonathan R. et al. "Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models" vol. 11, no. 5, 2015 Export RIS Citation Information.

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Karr, Jonathan R. ;

Williams, Alex H.

May 28 2015 | PLoS Comput Biol. 2015; 11(5).

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Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. Howe...
High-sensitivity measurements of multiple kinase activities in live single cells

CITE Title : High-sensitivity measurements of multiple kinase activities in live single cells Personal Author(s) : Regot, Sergi;Hughey, Jacob J.;Bajar, Bryce T.;Carrasco, Silvia;Covert, Markus W.; Published Date : Jun 19 2014 Source : Cell. 2014; 157(7):1724-1734. URL : https://stacks.cdc.gov/view/cdc/30035 Regot, Sergi et al. (2014). High-sensitivity measurements of multiple kinase activities in live single cells. 157(7). Regot, Sergi et al. "High-sensitivity measurements of multiple kinase activities in live single cells" 157, no. 7 (2014) Regot, Sergi et al. "High-sensitivity measurements of multiple kinase activities in live single cells" vol. 157, no. 7, 2014 Export RIS Citation Information.

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Regot, Sergi ;

Hughey, Jacob J.

Jun 19 2014 | Cell. 2014; 157(7):1724-1734.

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Increasing evidence has shown that population dynamics are qualitatively different from single-cell behaviors. Reporters to probe dynamic, single-cell...
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

CITE Title : WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions Personal Author(s) : Karr, Jonathan R.;Phillips, Nolan C.;Covert, Markus W.; Published Date : Sep 16 2014 Source : Database (Oxford). 2014; 2014. URL : https://stacks.cdc.gov/view/cdc/32168 Karr, Jonathan R. et al. (2014). WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. 2014 Karr, Jonathan R. and Phillips, Nolan C. and Covert, Markus W. "WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions" 2014 (2014) Karr, Jonathan R. et al. "WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions" vol. 2014, 2014 Export RIS Citation Information.

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Karr, Jonathan R. ;

Phillips, Nolan C.

Sep 16 2014 | Database (Oxford). 2014; 2014.

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Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-...
Why build whole-cell models?

CITE Title : Why build whole-cell models? Personal Author(s) : Carrera, Javier;Covert, Markus W.; Published Date : Oct 21 2015 Source : Trends Cell Biol. 25(12):719-722. URL : https://stacks.cdc.gov/view/cdc/38310 Carrera, Javier and Covert, Markus W. (2015). Why build whole-cell models?. 25(12). Carrera, Javier and Covert, Markus W. "Why build whole-cell models?" 25, no. 12 (2015) Carrera, Javier and Covert, Markus W. "Why build whole-cell models?" vol. 25, no. 12, 2015 Export RIS Citation Information.

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Carrera, Javier ;

Covert, Markus W.

Oct 21 2015 | Trends Cell Biol. 25(12):719-722.

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Our ability to build computational models that account for all known gene functions in a cell has increased dramatically. But why build whole-cell mod...
NetworkPainter: dynamic intracellular pathway animation in Cytobank

CITE Title : NetworkPainter: dynamic intracellular pathway animation in Cytobank Personal Author(s) : Karr, Jonathan R;Guturu, Harendra;Chen, Edward Y;Blair, Stuart L;Irish, Jonathan M;Kotecha, Nikesh;Covert, Markus W; Published Date : May 25 2015 Source : BMC Bioinformatics. 16(1). URL : https://stacks.cdc.gov/view/cdc/31977 Karr, Jonathan R et al. (2015). NetworkPainter: dynamic intracellular pathway animation in Cytobank. 16(1). Karr, Jonathan R et al. "NetworkPainter: dynamic intracellular pathway animation in Cytobank" 16, no. 1 (2015) Karr, Jonathan R et al. "NetworkPainter: dynamic intracellular pathway animation in Cytobank" vol. 16, no. 1, 2015 Export RIS Citation Information.

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Karr, Jonathan R ;

Guturu, Harendra

May 25 2015 | BMC Bioinformatics. 16(1).

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BackgroundHigh-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data...
Incorporation of Flexible Objectives and Time-Linked Simulation with Flux Balance Analysis

CITE Title : Incorporation of Flexible Objectives and Time-Linked Simulation with Flux Balance Analysis Personal Author(s) : Birch, Elsa W.;Udell, Madeleine;Covert, Markus W.; Published Date : Dec 17 2013 Source : J Theor Biol. 2013; 345:12-21. URL : https://stacks.cdc.gov/view/cdc/29858 Birch, Elsa W. et al. (2013). Incorporation of Flexible Objectives and Time-Linked Simulation with Flux Balance Analysis. 345 Birch, Elsa W. and Udell, Madeleine and Covert, Markus W. "Incorporation of Flexible Objectives and Time-Linked Simulation with Flux Balance Analysis" 345 (2013) Birch, Elsa W. et al. "Incorporation of Flexible Objectives and Time-Linked Simulation with Flux Balance Analysis" vol. 345, 2013 Export RIS Citation Information.

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Birch, Elsa W. ;

Udell, Madeleine

Dec 17 2013 | J Theor Biol. 2013; 345:12-21.

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We present two modifications of the flux balance analysis (FBA) metabolic modeling framework which relax implicit assumptions of the biomass reaction....
WholeCellViz: data visualization for whole-cell models

CITE Title : WholeCellViz: data visualization for whole-cell models Personal Author(s) : Lee, Ruby;Karr, Jonathan R;Covert, Markus W; Published Date : Aug 21 2013 Source : BMC Bioinformatics. 2013; 14:253. URL : https://stacks.cdc.gov/view/cdc/22566 Lee, Ruby et al. (2013). WholeCellViz: data visualization for whole-cell models. 14 Lee, Ruby and Karr, Jonathan R and Covert, Markus W "WholeCellViz: data visualization for whole-cell models" 14 (2013) Lee, Ruby et al. "WholeCellViz: data visualization for whole-cell models" vol. 14, 2013 Export RIS Citation Information.

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Lee, Ruby ;

Karr, Jonathan R

Aug 21 2013 | BMC Bioinformatics. 2013; 14:253.

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BackgroundWhole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and othe...
Accelerated discovery via a whole-cell model

CITE Title : Accelerated discovery via a whole-cell model Personal Author(s) : Sanghvi, Jayodita C.;Regot, Sergi;Carrasco, Silvia;Karr, Jonathan R.;Gutschow, Miriam V.;Bolival, Benjamin;Covert, Markus W.; Published Date : Nov 03 2013 Source : Nat Methods. 10(12):1192-1195. URL : https://stacks.cdc.gov/view/cdc/29799 Sanghvi, Jayodita C. et al. (2013). Accelerated discovery via a whole-cell model. 10(12). Sanghvi, Jayodita C. et al. "Accelerated discovery via a whole-cell model" 10, no. 12 (2013) Sanghvi, Jayodita C. et al. "Accelerated discovery via a whole-cell model" vol. 10, no. 12, 2013 Export RIS Citation Information.

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Sanghvi, Jayodita C. ;

Regot, Sergi

Nov 03 2013 | Nat Methods. 10(12):1192-1195.

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To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimenta...
WholeCellKB: model organism databases for comprehensive whole-cell models

CITE Title : WholeCellKB: model organism databases for comprehensive whole-cell models Personal Author(s) : Karr, Jonathan R.;Sanghvi, Jayodita C.;Macklin, Derek N.;Arora, Abhishek;Covert, Markus W.; Published Date : Nov 21 2012 Source : Nucleic Acids Res. 2012; 41(Database issue):D787-D792. URL : https://stacks.cdc.gov/view/cdc/22629 Karr, Jonathan R. et al. (2012). WholeCellKB: model organism databases for comprehensive whole-cell models. 41 Karr, Jonathan R. et al. "WholeCellKB: model organism databases for comprehensive whole-cell models" 41 (2012) Karr, Jonathan R. et al. "WholeCellKB: model organism databases for comprehensive whole-cell models" vol. 41, 2012 Export RIS Citation Information.

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Karr, Jonathan R. ;

Sanghvi, Jayodita C.

Nov 21 2012 | Nucleic Acids Res. 2012; 41(Database issue):D787-D792.

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Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors. Whole-cell model development requires comprehensive mode...
Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation

CITE Title : Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation Personal Author(s) : Birch, Elsa W.;Ruggero, Nicholas A.;Covert, Markus W.; Published Date : Oct 18 2012 Source : PLoS Comput Biol. 2012; 8(10). URL : https://stacks.cdc.gov/view/cdc/22686 Birch, Elsa W. et al. (2012). Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation. 8(10). Birch, Elsa W. and Ruggero, Nicholas A. and Covert, Markus W. "Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation" 8, no. 10 (2012) Birch, Elsa W. et al. "Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation" vol. 8, no. 10, 2012 Export RIS Citation Information.

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Birch, Elsa W. ;

Ruggero, Nicholas A.

Oct 18 2012 | PLoS Comput Biol. 2012; 8(10).

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Viral replication relies on host metabolic machinery and precursors to produce large numbers of progeny - often very rapidly. A fundamental example is...