Research reports

  1. Lang PF, Chebaro Y & Karr JR. BpForms: a toolkit for concretely describing modified DNA, RNA and proteins. arXiv 1903.10042 (2019).
  2. Cokelaer T, Bansal M, Bare C, Bila E, Bot BM, Neto EC, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner R, Menden MP, Meyer P, Nore R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G & Saez-Rodriguez J. DREAMTools: a Python package for scoring collaborative challenges. F1000Res 4, 1030 (2015).
  3. Kazakiewicz D*, Karr JR*,†, Langner KM & Plewczynski D. Combined systems and structural modeling repositions antibiotics for Mycoplasma genitalium. Comput Biol Chem pii, S1476-9271(15)30089-X (2015).
  4. Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA & Meyer P. Summary of the DREAM8 parameter estimation challenge: Toward parameter identification for whole-cell models. PLoS Comput Biol 11, e1004096 (2015).
  5. Karr JR, Guturu HG, Chen E, Blair S, Irish JM, Kotech N & Covert MW. NetworkPainter: Dynamic intracellular pathway animation in Cytobank. BMC Bioinformatics 16, 172 (2015).
  6. Chang R, Karr JR & Schadt EE. Causal inference in biology networks with integrated belief propagation. Pac Symp Biocomput, 359–70 (2015).
  7. Karr JR*, Phillips NC* & Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database 2014, bau095 (2014).
  8. Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B & Covert MW. Accelerated discovery via a whole-cell model. Nat Methods 10, 1192–1195 (2013).
  9. Lee R*, Karr JR* & Covert MW. WholeCellViz: data visualization for whole-cell models. BMC Bioinformatics 14, 253 (2013).
  10. Purcell O, Jain B, Karr JR, Covert MW & Lu T. Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112 (2013).
  11. Karr JR, Sanghvi JC, Macklin DN, Arora A & Covert MW. WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Res 41, D787–792 (2013).
  12. 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 (2012).
  13. Covert MW, Xiao N, Chen TJ & Karr JR. Integrated flux balance analysis model of Escherichia coli. Bioinformatics 24, 2044–50 (2008).

Reviews & perspectives

  1. Karr JR. Forward to Theoretical and Applied Aspects of Systems Biology 27 (2018).
  2. Goldberg AP*, Szigeti B*, Chew YH*, Sekar JAP*, Roth YD & Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 51, 97–102 (2018).
  3. Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC & Karr JR. A blueprint for human whole-cell modeling. Curr Opin Syst Biol 7, 8–15 (2018).
  4. Medley JK, Goldberg AP & Karr JR. Guidelines for reproducibly building and simulating systems biology models. IEEE Trans Biomed Eng 63, 2015–2020 (2016).
  5. Waltemath D*, Karr JR* et al. Toward community standards and software for whole-cell modeling. IEEE Trans Biomed Eng 63, 2007–2014 (2016).
  6. Goldberg AP, Chew YH & Karr JR. Toward scalable whole-cell modeling of human cells. ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, 259–262 (2016).
  7. Kovatch P, Costa A, Chen R, Klein R, Costa KD, Hajjar RJ, Fayad Z, Margolies L, Mendelson D, Yankelevitz D, Goldberg AP, Karr JR, Rice JJ & Gurev V. The potential for exascale to transform healthcare. Supercomputing Frontiers (2016).
  8. Karr JR, Takahasi K & Funahashi A. The principles of whole-cell modeling. Curr Opin Microbiol 27, 18–24 (2015).

Reports and requests for information

  1. Karr JR, Lluch-Senar M, Kastelic D, Serrano L & Sauro HM. Initiatives to build a whole-cell modeling community: 2019 update (2019).
  2. Karr JR, Lluch-Senar M, Serrano L & Kastelic D. The 2017 Whole-Cell Modeling Summer School (2017).
  3. Karr JR, Lluch-Senar M, Serrano L & Carrera J. The 2016 Whole-Cell Modeling Summer School (2016).
  4. Goldberg AP & Karr JR. Whole-cell model simulations for medicine and bioengineering. In response to NIGMS Request for Information on Science Drivers Requiring Capable Exascale High Performance Computing (2015).


  1. Karr JR & Goldberg AP. An introduction to whole-cell modeling. (2017).

Lay articles

  1. Karr JR, Chew YH & Goldberg AP. Whole-cell computational models can predict how genes influence behavior. Atlas of Science (2015).

Source code and other supplementary material
*These authors contributed equally to this work
Corresponding author

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