All Stories

  1. Organizing genome engineering for the gigabase scale

    Article • Nature Communications, February 2020, Springer Science + Business Media

    Jonathan Karr

  2. A blueprint for human whole-cell modeling

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  3. Guidelines for Reproducibly Building and Simulating Systems Biology Models

    Article • IEEE Transactions on Biomedical Engineering, October 2016, Institute of Electrical & Electronics Engineers (IEEE)

    Jonathan Karr

  4. Toward Community Standards and Software for Whole-Cell Modeling

    Article • IEEE Transactions on Biomedical Engineering, October 2016, Institute of Electrical & Electronics Engineers (IEEE)

    Jonathan Karr

  5. Toward Scalable Whole-Cell Modeling of Human Cells

    Article • May 2016, ACM (Association for Computing Machinery)

    Jonathan Karr

  6. A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

    Article • Computational Biology and Chemistry, December 2015, Elsevier

    Jonathan Karr

  7. DREAMTools: a Python package for scoring collaborative challenges

    Article • F1000Research, October 2015, Faculty of 1000, Ltd.

    Jonathan Karr, Professor Julio Saez-Rodriguez, Raquel Norel, Brian Bot

  8. The principles of whole-cell modeling

    Article • Current Opinion in Microbiology, October 2015, Elsevier

    Jonathan Karr

  9. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

    Article • PLoS Computational Biology, May 2015, PLOS

    Jonathan Karr

  10. NetworkPainter: dynamic intracellular pathway animation in Cytobank

    Article • BMC Bioinformatics, May 2015, Springer Science + Business Media

    Jonathan Karr

  11. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

    Article • Database, September 2014, Oxford University Press (OUP)

    Jonathan Karr

  12. Accelerated discovery via a whole-cell model

    Article • Nature Methods, November 2013, Nature

    Jonathan Karr

  13. Towards a whole-cell modeling approach for synthetic biology

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, June 2013, American Institute of Physics

    Jonathan Karr

  14. WholeCellViz: data visualization for whole-cell models

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Jonathan Karr

  15. WholeCellKB: model organism databases for comprehensive whole-cell models

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    Jonathan Karr

  16. A Whole-Cell Computational Model Predicts Phenotype from Genotype

    Article • Cell, July 2012, Elsevier

    Jonathan Karr

  17. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

    Article • Bioinformatics, July 2008, Oxford University Press (OUP)

    Jonathan Karr