| A whole-cell computational model predicts phenotype from genotype JR Karr, JC Sanghvi, DN Macklin, MV Gutschow, JM Jacobs, B Bolival, ... Cell 150 (2), 389-401, 2012 | 1591 | 2012 |
| Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli MW Covert, N Xiao, TJ Chen, JR Karr Bioinformatics 24 (18), 2044-2050, 2008 | 393 | 2008 |
| SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020 | 239 | 2020 |
| Towards a whole-cell modeling approach for synthetic biology O Purcell, B Jain, JR Karr, MW Covert, TK Lu Chaos 23 (2), 025112, 2013 | 101 | 2013 |
| The principles of whole-cell modeling JR Karr, K Takahashi, A Funahashi Current Opinion in Microbiology 27, 18-24, 2015 | 87 | 2015 |
| Accelerated discovery via a whole-cell model JC Sanghvi, S Regot, S Carrasco, JR Karr, MV Gutschow, B Bolival Jr, ... Nature Methods 10 (12), 1192, 2013 | 83 | 2013 |
| A blueprint for human whole-cell modeling B Szigeti, YD Roth, JAP Sekar, AP Goldberg, SC Pochiraju, JR Karr Current Opinion in Systems Biology 7, 8-15, 2018 | 80 | 2018 |
| Emerging whole-cell modeling principles and methods AP Goldberg, B Szigeti, YH Chew, JAP Sekar, YD Roth, JR Karr Current Opinion in Biotechnology 51, 97-102, 2018 | 78 | 2018 |
| WholeCellKB: model organism databases for comprehensive whole-cell models JR Karr, JC Sanghvi, DN Macklin, A Arora, MW Covert Nucleic Acids Research 41 (D1), D787-D792, 2012 | 67 | 2012 |
| Toward community standards and software for whole-cell modeling D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ... IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016 | 65 | 2016 |
| Building structural models of a whole mycoplasma cell M Maritan, L Autin, J Karr, MW Covert, AJ Olson, DS Goodsell Journal of molecular biology 434 (2), 167351, 2022 | 48 | 2022 |
| Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models JR Karr, AH Williams, JD Zucker, A Raue, B Steiert, J Timmer, C Kreutz, ... PLoS Computational Biology 11 (5), 2015 | 46 | 2015 |
| Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology L Marucci, M Barberis, J Karr, O Ray, PR Race, M de Souza Andrade, ... Frontiers in Bioengineering and Biotechnology 8, 942, 2020 | 39 | 2020 |
| Best practices for making reproducible biochemical models VL Porubsky, AP Goldberg, AK Rampadarath, DP Nickerson, JR Karr, ... Cell systems 11 (2), 109-120, 2020 | 35 | 2020 |
| Guidelines for reproducibly building and simulating systems biology models JK Medley, AP Goldberg, JR Karr IEEE Transactions on Biomedical Engineering 63 (10), 2015-2020, 2016 | 34 | 2016 |
| WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions JR Karr, NC Phillips, MW Covert Database 2014, bau095, 2014 | 30 | 2014 |
| DREAMTools: a Python package for scoring collaborative challenges T Cokelaer, M Bansal, C Bare, E Bilal, BM Bot, EC Neto, F Eduati, ... F1000Research 4, 1030, 2016 | 29 | 2016 |
| WholeCellViz: data visualization for whole-cell models R Lee, JR Karr, MW Covert BMC Bioinformatics 14 (1), 253, 2013 | 28 | 2013 |
| Organizing genome engineering for the gigabase scale BA Bartley, J Beal, JR Karr, EA Strychalski Nature Communicatons 11, 689, 2020 | 25 | 2020 |
| BioSimulators: a central registry of simulation engines and services for recommending specific tools B Shaikh, LP Smith, D Vasilescu, G Marupilla, M Wilson, E Agmon, ... Nucleic acids research 50 (W1), W108-W114, 2022 | 22 | 2022 |
Markus CovertStanford UniversityVerified email at stanford.edu
