All Stories

  1. Verification and reproducible curation of the BioModels repository

    Article • PLoS Computational Biology, December 2025, PLOS

    Jonathan Karr

  2. Verification and reproducible curation of the BioModels repository

    Article • January 2025, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  3. The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

    Article • Journal of Integrative Bioinformatics, March 2024, De Gruyter

    Jonathan Karr

  4. Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm

    Article • Biophysical Journal, December 2021, Elsevier

    Jonathan Karr

  5. Centralizing data to unlock whole-cell models

    Article • Current Opinion in Systems Biology, September 2021, Elsevier

    Jonathan Karr

  6. Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

    Article • Current Opinion in Systems Biology, September 2021, Elsevier

    Jonathan Karr

  7. RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

    Article • Nucleic Acids Research, May 2021, Oxford University Press (OUP)

    Jonathan Karr

  8. runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  9. Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology

    Article • January 2021, Elsevier

    Jonathan Karr

  10. Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  11. Furthering genome design using models and algorithms

    Article • Current Opinion in Systems Biology, December 2020, Elsevier

    Jonathan Karr

  12. DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python

    Article • The Journal of Open Source Software, November 2020, The Open Journal

    Jonathan Karr

  13. Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Jonathan Karr

  14. Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  15. Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  16. BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks

    Article • Genome Biology, May 2020, Springer Science + Business Media

    Jonathan Karr

  17. Organizing genome engineering for the gigabase scale

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

    Jonathan Karr

  18. Emerging whole-cell modeling principles and methods

    Article • Current Opinion in Biotechnology, June 2018, Elsevier

    Jonathan Karr

  19. A blueprint for human whole-cell modeling

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Jonathan Karr

  20. 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

  21. 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

  22. Toward Scalable Whole-Cell Modeling of Human Cells

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

    Jonathan Karr

  23. DREAMTools: a Python package for scoring collaborative challenges

    Article • F1000Research, April 2016, Faculty of 1000, Ltd.

    Professor Julio Saez-Rodriguez, Jonathan Karr

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

    Article • Computational Biology and Chemistry, December 2015, Elsevier

    Jonathan Karr

  25. 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

  26. The principles of whole-cell modeling

    Article • Current Opinion in Microbiology, October 2015, Elsevier

    Jonathan Karr

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

    Article • PLoS Computational Biology, May 2015, PLOS

    Jonathan Karr

  28. NetworkPainter: dynamic intracellular pathway animation in Cytobank

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

    Jonathan Karr

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

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

    Jonathan Karr

  30. Accelerated discovery via a whole-cell model

    Article • Nature Chemical Biology, November 2013, Nature

    Jonathan Karr

  31. 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

  32. WholeCellViz: data visualization for whole-cell models

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

    Jonathan Karr

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

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

    Jonathan Karr

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

    Article • Cell, July 2012, Elsevier

    Jonathan Karr

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

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

    Jonathan Karr