Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. - Markus W. Covert; Nan Xiao; Tiffany J. Chen; Jonathan R. Karr (Bioinform., 2008)

A dynamic network of transcription in LPS-treated human subjects. - Junhee Seok; Wenzhong Xiao; Lyle L. Moldawer; Ronald W. Davis; Markus W. Covert (BMC Syst. Biol., 2009)

Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation. - Elsa W. Birch; Nicholas A. Ruggero; Markus W. Covert (PLoS Comput. Biol., 2012)

WholeCellViz: data visualization for whole-cell models. - Ruby Lee; Jonathan R. Karr; Markus W. Covert (BMC Bioinform., 2013)

WholeCellKB: model organism databases for comprehensive whole-cell models. - Jonathan R. Karr; Jayodita C. Sanghvi; Derek N. Macklin; Abhishek Arora 001; Markus W. Covert (Nucleic Acids Res., 2013)

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. - Jonathan R. Karr; Nolan C. Phillips; Markus W. Covert (Database J. Biol. Databases Curation, 2014)

NetworkPainter: dynamic intracellular pathway animation in Cytobank. - Jonathan R. Karr; Harendra Guturu; Edward Y. Chen; Stuart L. Blair; Jonathan M. Irish; Nikesh Kotecha; Markus W. Covert (BMC Bioinform., 2015)

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. - Jonathan R. Karr; Alex H. Williams; Jeremy D. Zucker; Andreas Raue; Bernhard Steiert; Jens Timmer; Clemens Kreutz; Simon Wilkinson; Brandon A. Allgood; Brian M. Bot; Bruce R. Hoff; Michael R. Kellen; et al. (PLoS Comput. Biol., 2015)

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. - David A. Van Valen; Takamasa Kudo; Keara M. Lane; Derek N. Macklin; Nicolas T. Quach; Mialy M. DeFelice; Inbal Maayan; Yu Tanouchi; Euan A. Ashley; Markus W. Covert (PLoS Comput. Biol., 2016)

Vivarium: an interface and engine for integrative multiscale modeling in computational biology. - Eran Agmon; Ryan K. Spangler; Christopher J. Skalnik; William Poole; Shayn M. Peirce; Jerry H. Morrison; Markus W. Covert (Bioinform., 2022)

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. - Christopher J. Skalnik; Sean Y. Cheah; Mica Y. Yang; Mattheus B. Wolff; Ryan K. Spangler; Lee Talman; Jerry H. Morrison; Shayn M. Peirce; Eran Agmon; Markus W. Covert (PLoS Comput. Biol., 2023)