• A reappraisal of how to build modular, reusable models of biological systems
    Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL and Gennari JH
    PLoS Comput Biol 10, 10: e1003849 (2014)
  • A whole-cell computational model predicts phenotype from genotype
    Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI and Covert MW
    Cell 150, 2: 389-401 (2012)
  • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL and Hucka M
    Nucleic Acids Res 34, suppl 1: D689-D691 (2006)
  • Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation
    Blinov ML, Ruebenacker O and Moraru II
    IET Syst Biol 2, 5: 363-368 (2008)
  • Guidelines for reproducibly building and simulating systems biology models
    Medley JK, Goldberg AP and Karr JR
    IEEE Trans Biomed Eng, (2016)
  • libRoadRunner: a high performance SBML simulation and analysis library
    Somogyi ET, Bouteiller JM, Glazier JA, König M, Medley JK, Swat MH and Sauro HM
    Bioinformatics 31, 20: 3315-3321 (2015)
  • Minimum information requested in the annotation of biochemical models (MIRIAM)
    Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD and Wanner BL
    Nature Biotechnol 23, 12: 1509-1515 (2005)
  • Modeling without borders: creating and annotating VCell models using the web
    Blinov ML, Ruebenacker O, Schaff JC and Moraru II
    Int Symp Bioinformatics Research Applications, 3-17 (2010)
  • Multiple ontologies in action: composite annotations for biosimulation models
    Gennari JH, Neal ML, Galdzicki M and Cook DL
    J Biomed Informatics 44, 1: 146-154 (2011)
  • Spatial modeling of cell signaling networks
    Cowan AE, Moraru II, Schaff JC, Slepchenko BM and Loew LM
    Meth Cell Biol 110, 195 (2012)
  • Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
    Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA and others
    PLoS Comput Biol 11, 5: e1004096 (2015)
  • WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions
    Karr JR, Phillips NC and Covert MW
    Database, pii: bau095 (2014)
  • WholeCellViz: data visualization for whole-cell models
    Lee R, Karr JR and Covert MW
    BMC Bioinformatics 14, 253 (2013)
  • Virtual Cell (VCell) Modeling and Analysis Platform
    Moraru II
    Encyc Syst Biol, 2342–2347 (2013)
  • Virtual Cell modelling and simulation software environment
    Moraru II, Schaff JC, Slepchenko BM, Blinov ML, Morgan F, Lakshminarayana A, Gao F, Li Y and Loew LM
    IET Syst Biol 2, 5: 352–362 (2008)
  • Tellurium: An extensible python-based modeling environment for systems and synthetic biology
    Choi K, Medley JK, König M, Stocking K, Smith L, Gu S and Sauro HM
    bioRxiv: 054601 (2016)
  • The principles of whole-cell modeling
    Karr JR, Takahashi K and Funahashi A
    Curr Opin Microbiol 27: 18-24 (2015)
  • The Systems Biology Graphical Notation
    Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K and Kitano H
    Nature Biotechnol 27, 8: 735-741 (2009)
  • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J and SBML Forum
    Bioinformatics 19, 4: 524-531 (2003)
  • The Virtual Cell project
    Loew LM, Schaff JC, Slepchenko BM and Moraru II
    Systems Biomedicine, 273 (2010)
  • Toward scalable whole-cell modeling of human cells
    Goldberg AP, Chew YH and Karr JR
    Principles of Advanced Discrete Simulation (2016)
  • WholeCellKB: model organism databases for comprehensive whole-cell models
    Karr JR, Sanghvi JC, Macklin DN, Arora A and Covert MW
    Nucleic Acids Res 41, Database issue: D787-792 (2012)