Jonathan Karr - Publications

Biophysics Stanford University, Palo Alto, CA 

14 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Medley JK, Goldberg A, Karr JR. Guidelines for reproducibly building and simulating systems biology models. Ieee Transactions On Bio-Medical Engineering. PMID 27429432 DOI: 10.1109/TBME.2016.2591960  0.56
2016 Goldberg AP, Chew YH, Karr JR. Toward scalable whole-cell modeling of human cells Sigsim-Pads 2016 - Proceedings of the 2016 Annual Acm Conference On Principles of Advanced Discrete Simulation. 259-262. DOI: 10.1145/2901378.2901402  0.56
2015 Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Norel R, et al. DREAMTools: a Python package for scoring collaborative challenges. F1000research. 4: 1030. PMID 27134723 DOI: 10.12688/F1000Research.7118.2  0.56
2015 Kazakiewicz D, Karr JR, Langner KM, Plewczynski D. A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. Computational Biology and Chemistry. PMID 26271684 DOI: 10.1016/J.Compbiolchem.2015.07.007  0.56
2015 Karr JR, Takahashi K, Funahashi A. The principles of whole-cell modeling. Current Opinion in Microbiology. 27: 18-24. PMID 26115539 DOI: 10.1016/j.mib.2015.06.004  0.56
2015 Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, et al. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. Plos Computational Biology. 11: e1004096. PMID 26020786 DOI: 10.1371/Journal.Pcbi.1004096  0.56
2015 Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW. NetworkPainter: dynamic intracellular pathway animation in Cytobank. Bmc Bioinformatics. 16: 172. PMID 26003204 DOI: 10.1186/S12859-015-0602-4  0.56
2014 Karr JR, Phillips NC, Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database : the Journal of Biological Databases and Curation. 2014. PMID 25231498 DOI: 10.1093/Database/Bau095  0.56
2013 Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B, Covert MW. Accelerated discovery via a whole-cell model. Nature Methods. 10: 1192-5. PMID 24185838 DOI: 10.1038/Nmeth.2724  0.56
2013 Lee R, Karr JR, Covert MW. WholeCellViz: data visualization for whole-cell models. Bmc Bioinformatics. 14: 253. PMID 23964998 DOI: 10.1186/1471-2105-14-253  0.56
2013 Purcell O, Jain B, Karr JR, Covert MW, Lu TK. Towards a whole-cell modeling approach for synthetic biology. Chaos (Woodbury, N.Y.). 23: 025112. PMID 23822510 DOI: 10.1063/1.4811182  0.56
2013 Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Research. 41: D787-92. PMID 23175606 DOI: 10.1093/Nar/Gks1108  0.56
2012 Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 150: 389-401. PMID 22817898 DOI: 10.1016/J.Cell.2012.05.044  0.56
2008 Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics (Oxford, England). 24: 2044-50. PMID 18621757 DOI: 10.1093/Bioinformatics/Btn352  0.56
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