Think simulation - think experiment: the virtual cell paradigm. - Ion I. Moraru; James C. Schaff; Leslie M. Loew (WSC, 2006)

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes. - Michael L. Blinov; Ion I. Moraru (BIBE, 2007)

Kinetic Modeling Using BioPAX Ontology. - Oliver Ruebenacker; Ion I. Moraru; James C. Schaff; Michael L. Blinov (BIBM, 2007)

Modeling without Borders: Creating and Annotating VCell Models Using the Web. - Michael L. Blinov; Oliver Ruebenacker; James C. Schaff; Ion I. Moraru (ISBRA, 2010)

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. - Dagmar Waltemath; Richard R. Adams; Frank T. Bergmann; Michael Hucka; Fedor A. Kolpakov; Andrew K. Miller; Ion I. Moraru; David P. Nickerson; Sven Sahle; Jacky L. Snoep; Nicolas Le Novère (BMC Syst. Biol., 2011)

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. - Sherry-Ann Brown; Ion I. Moraru; James C. Schaff; Leslie M. Loew (J. Comput. Neurosci., 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. - Michael L. Blinov; James C. Schaff; Oliver Ruebenacker; Xintao Wei; Dan Vasilescu; Fei Gao; Frank Morgan; Li Ye; Anuradha Lakshminarayana; Ion I. Moraru; Leslie M. Loew (Bioinform., 2014)

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. - Lucian Paul Smith; Michael Hucka; Stefan Hoops; Andrew Finney; Martin Ginkel; Chris J. Myers; Ion I. Moraru; Wolfram Liebermeister (J. Integr. Bioinform., 2015)

Rule-based modeling with Virtual Cell. - James C. Schaff; Dan Vasilescu; Ion I. Moraru; Leslie M. Loew; Michael L. Blinov (Bioinform., 2016)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). - Frank T. Bergmann; Jonathan Cooper; Matthias König 003; Ion I. Moraru; David P. Nickerson; Nicolas Le Novère; Brett G. Olivier; Sven Sahle; Lucian P. Smith; Dagmar Waltemath (J. Integr. Bioinform., 2018)

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. - Bilal Shaikh; Gnaneswara Marupilla; Mike Wilson; Michael L. Blinov; Ion I. Moraru; Jonathan R. Karr (Nucleic Acids Res., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)