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

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)

Causal Inference in Biology Networks with Integrated Belief Propagation. - Rui Chang; Jonathan R. Karr; Eric E. Schadt (Pacific Symposium on Biocomputing, 2015)

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)

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. - Denis Kazakiewicz; Jonathan R. Karr; Karol M. Langner; Dariusz Plewczynski (Comput. Biol. Chem., 2015)

DREAMTools: a Python package for scoring collaborative challenges. - Thomas Cokelaer; Mukesh Bansal; Christopher Bare; Erhan Bilal; Brian M. Bot; Elias Chaibub Neto; Federica Eduati; Mehmet Gönen; Steven M. Hill; Bruce R. Hoff; Jonathan R. Karr; Robert Küffner; et al. (F1000Research, 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)

Toward Scalable Whole-Cell Modeling of Human Cells. - Arthur P. Goldberg; Yin Hoon Chew; Jonathan R. Karr (SIGSIM-PADS, 2016)

Guidelines for Reproducibly Building and Simulating Systems Biology Models. - J. Kyle Medley; Arthur P. Goldberg; Jonathan R. Karr (IEEE Trans. Biomed. Eng., 2016)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

Structured spreadsheets with ObjTables enable data reuse and integration. - Jonathan R. Karr; Wolfram Liebermeister; Arthur P. Goldberg; John A. P. Sekar; Bilal Shaikh (CoRR, 2020)

Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks. - Arthur P. Goldberg; John A. P. Sekar; Jonathan R. Karr (CoRR, 2020)

DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python. - Arthur P. Goldberg; Jonathan R. Karr (J. Open Source Softw., 2020)

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. - Alexander Mazein; Adrien Rougny; Jonathan R. Karr; Julio Saez-Rodriguez; Marek Ostaszewski; Reinhard Schneider 002 (Briefings Bioinform., 2021)

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. - Andreas Dräger; Tomás Helikar; Matteo Barberis; Marc R. Birtwistle; Laurence Calzone; Claudine Chaouiya; Jan Hasenauer; Jonathan R. Karr; Anna Niarakis; María Rodríguez Martínez; Julio Saez-Rodriguez; Juilee Thakar (Bioinform., 2021)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2021)

Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. - Yosef D. Roth; Zhouyang Lian; Saahith Pochiraju; Bilal Shaikh; Jonathan R. Karr (Nucleic Acids Res., 2021)

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. - Bilal Shaikh; Gnaneswara Marupilla; Mike Wilson; Michael L. Blinov; Ion I. Moraru; Jonathan R. Karr (Nucleic Acids Res., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2024)