Osmotic Forces and Gap Junctions in Spreading Depression: A Computational Model. - Bruce E. Shapiro (J. Comput. Neurosci., 2001)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. - Bruce E. Shapiro; Andre Levchenko; Elliot M. Meyerowitz; Barbara J. Wold; Eric Mjolsness (Bioinform., 2003)

MathSBML: a package for manipulating SBML-based biological models. - Bruce E. Shapiro; Michael Hucka; Andrew Finney; John Doyle 001 (Bioinform., 2004)

Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. - Henrik Jönsson; Marcus Heisler; G. Venugopala Reddy; Vikas Agrawal; Victoria Gor; Bruce E. Shapiro; Eric Mjolsness; Elliot M. Meyerowitz (ISMB (Supplement of Bioinformatics), 2005)

An enzyme mechanism language for the mathematical modeling of metabolic pathways. - Chin-Rang Yang; Bruce E. Shapiro; Eric Mjolsness; G. Wesley Hatfield (Bioinform., 2005)

Application of a Generalized Mwc Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes. - Tarek S. Najdi; Chin-Rang Yang; Bruce E. Shapiro; G. Wesley Hatfield; Eric Mjolsness (J. Bioinform. Comput. Biol., 2006)

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. - Nicolas Le Novère; Benjamin J. Bornstein; Alexander Broicher; Mélanie Courtot; Marco Donizelli; Harish Dharuri; Lu Li 002; Herbert M. Sauro; Maria J. Schilstra; Bruce E. Shapiro; Jacky L. Snoep; Michael Hucka (Nucleic Acids Res., 2006)

Pycellerator: an arrow-based reaction-like modelling language for biological simulations. - Bruce E. Shapiro; Eric Mjolsness (Bioinform., 2016)