A Whole-Cell Computational Model Predicts Phenotype from Genotype von Karr, Jonathan R., Sanghvi, Jayodita C., Macklin, Derek N., Gutschow, Miriam V., Jacobs, Jared M., Bolival, Benjamin, Assad-Garcia, Nacyra, Glass, John I., Covert, Markus W.

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Organizing genome engineering for the gigabase scale von Bartley, Bryan A., Beal, Jacob, Karr, Jonathan R., Strychalski, Elizabeth A.

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BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks von Lang, Paul F, Chebaro, Yassmine, Zheng, Xiaoyue, P Sekar, John A, Shaikh, Bilal, Natale, Darren A, Karr, Jonathan R

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The principles of whole-cell modeling von Karr, Jonathan R, Takahashi, Koichi, Funahashi, Akira

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Editorial: Computer-Aided Biodesign Across Scales von Gorochowski, Thomas E, Karr, Jonathan R, Parmeggiani, Fabio, Yordanov, Boyan

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

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Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm von Tourigny, David S., Goldberg, Arthur P., Karr, Jonathan R.

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Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior von Roth, Yosef D, Lian, Zhouyang, Pochiraju, Saahith, Shaikh, Bilal, Karr, Jonathan R

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Emerging whole-cell modeling principles and methods von Goldberg, Arthur P, Szigeti, Balázs, Chew, Yin Hoon, Sekar, John AP, Roth, Yosef D, Karr, Jonathan R

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RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats von Shaikh, Bilal, Marupilla, Gnaneswara, Wilson, Mike, Blinov, Michael L, Moraru, Ion I, Karr, Jonathan R

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Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli von Covert, Markus W., Xiao, Nan, Chen, Tiffany J., Karr, Jonathan R.

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Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling von Mazein, Alexander, Rougny, Adrien, Karr, Jonathan R, Saez-Rodriguez, Julio, Ostaszewski, Marek, Schneider, Reinhard

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SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems von Dräger, Andreas, Helikar, Tomáš, Barberis, Matteo, Birtwistle, Marc, Calzone, Laurence, Chaouiya, Claudine, Hasenauer, Jan, Karr, Jonathan R, Niarakis, Anna, Rodríguez Martínez, María, Saez-Rodriguez, Julio, Thakar, Juilee

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Accelerated discovery via a whole-cell model von Sanghvi, Jayodita C, Regot, Sergi, Carrasco, Silvia, Karr, Jonathan R, Gutschow, Miriam V, Bolival, Benjamin, Covert, Markus W

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WholeCellViz: data visualization for whole-cell models von Lee, Ruby, Karr, Jonathan R, Covert, Markus W

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WholeCellKB: model organism databases for comprehensive whole-cell models von Karr, Jonathan R, Sanghvi, Jayodita C, Macklin, Derek N, Arora, Abhishek, Covert, Markus W

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RBAtools: a programming interface for Resource Balance Analysis models von Bodeit, Oliver, Ben Samir, Inès, Karr, Jonathan R, Goelzer, Anne, Liebermeister, Wolfram

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Towards a whole-cell modeling approach for synthetic biology von Purcell, Oliver, Jain, Bonny, Karr, Jonathan R., Covert, Markus W., Lu, Timothy K.

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Best Practices for Making Reproducible Biochemical Models von Porubsky, Veronica L., Goldberg, Arthur P., Rampadarath, Anand K., Nickerson, David P., Karr, Jonathan R., Sauro, Herbert M.

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A blueprint for human whole-cell modeling von Szigeti, Balázs, Roth, Yosef D., Sekar, John A.P., Goldberg, Arthur P., Pochiraju, Saahith C., Karr, Jonathan R.

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