☰

Jonathan Karr - Publications

Affiliations: 
Biophysics Stanford University, Palo Alto, CA 
Tree Info Similar researchers PubMed Report error

26 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
2023 Bodeit O, Ben Samir I, Karr JR, Goelzer A, Liebermeister W. RBAtools: a programming interface for Resource Balance Analysis models. Bioinformatics Advances. 3: vbad056. PMID 37179703 DOI: 10.1093/bioadv/vbad056  0.32
2022 Karr J, Malik-Sheriff RS, Osborne J, Gonzalez-Parra G, Forgoston E, Bowness R, Liu Y, Thompson R, Garira W, Barhak J, Rice J, Torres M, Dobrovolny HM, Tang T, Waites W, et al. Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility. Frontiers in Systems Biology. 2. PMID 36909847 DOI: 10.3389/fsysb.2022.822606  0.346
2022 Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, ... ... Karr JR, et al. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research. PMID 35524558 DOI: 10.1093/nar/gkac331  0.311
2021 Smith LP, Bergmann FT, Garny A, Helikar T, Karr J, Nickerson D, Sauro H, Waltemath D, König M. The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. Journal of Integrative Bioinformatics. 18: 20210021. PMID 35330701 DOI: 10.1515/jib-2021-0021  0.349
2021 Maritan M, Autin L, Karr J, Covert MW, Olson AJ, Goodsell DS. Building Structural Models of a Whole Mycoplasma Cell. Journal of Molecular Biology. 434: 167351. PMID 34774566 DOI: 10.1016/j.jmb.2021.167351  0.709
2021 Tourigny DS, Goldberg AP, Karr JR. Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm. Biophysical Journal. PMID 34757076 DOI: 10.1016/j.bpj.2021.10.038  0.408
2021 Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics (Oxford, England). PMID 34179955 DOI: 10.1093/bioinformatics/btab229  0.318
2021 Shaikh B, Marupilla G, Wilson M, Blinov ML, Moraru II, Karr JR. RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. Nucleic Acids Research. PMID 34019658 DOI: 10.1093/nar/gkab411  0.401
2020 Roth YD, Lian Z, Pochiraju S, Shaikh B, Karr JR. Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. Nucleic Acids Research. PMID 33174603 DOI: 10.1093/nar/gkaa1008  0.336
2020 Porubsky VL, Goldberg AP, Rampadarath AK, Nickerson DP, Karr JR, Sauro HM. Best Practices for Making Reproducible Biochemical Models. Cell Systems. 11: 109-120. PMID 32853539 DOI: 10.1016/j.cels.2020.06.012  0.454
2020 Marucci L, Barberis M, Karr J, Ray O, Race PR, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt J, Seabrook R, Shaw W, Woods C. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Frontiers in Bioengineering and Biotechnology. 8: 942. PMID 32850764 DOI: 10.3389/Fbioe.2020.00942  0.453
2018 Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC, Karr JR. A blueprint for human whole-cell modeling. Current Opinion in Systems Biology. 7: 8-15. PMID 29806041 DOI: 10.1016/j.coisb.2017.10.005  0.456
2017 Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD, Karr JR. Emerging whole-cell modeling principles and methods. Current Opinion in Biotechnology. 51: 97-102. PMID 29275251 DOI: 10.1016/j.copbio.2017.12.013  0.559
2016 Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, et al. Toward community standards and software for whole-cell modeling. Ieee Transactions On Bio-Medical Engineering. PMID 27305665 DOI: 10.1109/Tbme.2016.2560762  0.479
2016 Karr J. Whole-cell models: combining genomics and dynamical modeling F1000research. 5. DOI: 10.7490/F1000Research.1113292.1  0.498
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  0.481
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  0.535
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  0.699
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  0.595
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  0.689
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  0.658
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  0.708
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  0.701
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  0.731
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  0.745
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  0.678
Show low-probability matches.