Articles

  1. Goldberg AP & Karr JR. Scalable, multi-algorithmic simulation of whole-cell models with WC-Sim. (In preparation).
  2. Karr JR, Liebermeister W, Goldberg AP, Sekar JAP & Shaikh B. Structured spreadsheets with ObjTables enable data reuse and integration. arXiv:2005.05227.
  3. Shaikh B, Marupilla G, Wilson M, Goldberg AP, Schaff JC, Blinov ML, Moraru II & Karr JR. BioSimulators: a unified ecosystem for reproducing and reusing computational models. (In preparation).
  4. Shaikh B, Freiburger AP, König M, Bergmann FT, Nickerson DP, Sauro HM, Blinov ML, Smith LP, Moraru II & Karr JR. SED-ML Validator: tool for debugging simulation experiments. arXiv:2106.00844 (In review).
  5. Karr JR, Sheriff R, Osborne J, Parra GG, Forgoston E, Bowness R, Liu Y, Thompson R, Garira W, Barhak J, Rice J, Torres M, Dobrovolny HM, Tang T, Waites W, Glazier J & Faeder JR. Model integration in computational biology: the role of reproducibility, credibility and utility. Cureus (In review).
  6. Tourigny DS, Goldberg AP & Karr JR. Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm. bioRxiv: 10.1101/2020.05.22.110577 (In review).
  7. Chew YH & Karr JR. Centralizing data to unlock whole-cell models. Current Opinion in Systems Biology 27100353 (2021).
  8. Blinov ML*, Gennari JH*, Karr JR*, Moraru II*, Nickerson DP* & Sauro HM*. Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology. Current Opinion in Systems Biology 27 100350 (2021).
  9. Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Martínez MR, Saez-Rodriguez J & Thakar J. Five years of SysMod: Creating a community for advancing data-intensive modeling. Bioinformatics 37, btab229 (2021).
  10. Gorochowski TE, Karr JR, Parmeggiani F & Yordanov B. Computer-Aided Biodesign Across Scales. Frontiers in Bioengineering and Biotechnology (2021).
  11. Shaikh B, Marupilla G, Wilson M, Blinov ML, Moraru II & Karr JR. runBioSimulations: an extensible web application that simulates a wide range of mathematical modeling frameworks, algorithms, and formats. Nucleic Acids Research 49, gkab411 (2021).
  12. Mazein A, Rougny A, Karr JR, Saez-Rodriguez J, Ostaszewski M & Schneider R. Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Briefings in Bioinformatics, bbab103 (2021).
  13. Goldberg AP & Karr JR. DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python. Journal of Open Source Software (2020).
  14. Roth YD*, Zhouyang Lian*, Saahith Pochiraju, Bilal Shaikh & Karr JR. Datanator: integrated database of molecular data that facilitates models of biochemical networks. Nucleic Acids Research (2020).
  15. Keating S, Waltemath D, König M, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology 16, e9110 (2020).
  16. Goldberg AP, Sekar JAP & Karr JR. Exact parallelization of the Stochastic Simulation Algorithm for scalable simulation of large biochemical networks. arXiv:2005.05295.
  17. Lang PF, Chebaro Y, Zheng X, Sekar JAP, Shaikh B, Natale DA & Karr JR. BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks. Genome Biology 21, 117 (2020).
  18. Rees-Garbutt J, Rightmyer J, Karr JR, Grierson C & Marucci L. Furthering genome design using models and algorithms. Current Opinion in Systems Biology 24, 120–126 (2020).
  19. Porubsky VL*, Goldberg AP*, Rampadarath AK, Nickerson DP, Karr JR & and Sauro HM. Best Practices for Making Reproducible Biochemical Models. Cell Systems 11, 2 109–120 (2020).
  20. Marucci L, Barberis M*, Karr JR*, Ray O*, Race PR*, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt S, 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 (2020).
  21. Bartley BA*,†, Beal J*,†, Karr JR*,† & Strychalski E*,†. Organizing genome engineering for the gigabase scale. Nature Communications 11, 689 (2020).
  22. Choi K, Karr JR & Sauro HM. Status and challenges of reproducibility in computational systems and synthetic biology. Systems Medicine: Integrative, Qualitative and Computational Approaches (2019).
  23. Karr JR. Forward to Theoretical and Applied Aspects of Systems Biology 27 (2018).
  24. Goldberg AP*, Szigeti B*, Chew YH*, Sekar JAP*, Roth YD & Karr JR. Emerging whole-cell modeling principles and methods. Current Opinion in Biotechnology 51, 97–102 (2018).
  25. 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 (2018).
  26. Medley JK, Goldberg AP & Karr JR. Guidelines for reproducibly building and simulating systems biology models. IEEE Transactions on Biomedical Engineering 63, 2015–2020 (2016).
  27. Waltemath D*, Karr JR* et al. Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering 63, 2007–2014 (2016).
  28. 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).
  29. 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).
  30. 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. F1000 Research 4, 1030 (2015).
  31. Kazakiewicz D*, Karr JR*,†, Langner KM & Plewczynski D. Combined systems and structural modeling repositions antibiotics for Mycoplasma genitalium. Computational Biology and Chemistry pii, S1476-9271(15)30089-X (2015).
  32. 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 Computational Biology 11, e1004096 (2015).
  33. Karr JR, Takahasi K & Funahashi A. The principles of whole-cell modeling. Current Opinion in Microbiology 27, 18–24 (2015).
  34. 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).
  35. Chang R, Karr JR & Schadt EE. Causal inference in biology networks with integrated belief propagation. Pacific Symposium on Biocomputing, 359–70 (2015).
  36. Karr JR*, Phillips NC* & Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database 2014, bau095 (2014).
  37. Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B & Covert MW. Accelerated discovery via a whole-cell model. Nature Methods 10, 1192–1195 (2013).
  38. Lee R*, Karr JR* & Covert MW. WholeCellViz: data visualization for whole-cell models. BMC Bioinformatics 14, 253 (2013).
  39. Purcell O, Jain B, Karr JR, Covert MW & Lu T. Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112 (2013).
  40. Karr JR, Sanghvi JC, Macklin DN, Arora A & Covert MW. WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Research 41, D787–792 (2013).
  41. 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).
  42. Covert MW, Xiao N, Chen TJ & Karr JR. Integrated flux balance analysis model of Escherichia coli. Bioinformatics 24, 2044–50 (2008).

Reports

  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).

Primers

  1. Karr JR & Goldberg AP. An introduction to whole-cell modeling. https://docs.karrlab.org/intro_to_wc_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).


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

View publications on PubMed | Google Scholar