Bruce E. Shapiro
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, ...
Bioinformatics 19 (4), 524-531, 2003
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
N Le Novere, B Bornstein, A Broicher, M Courtot, M Donizelli, H Dharuri, ...
Nucleic acids research 34 (suppl_1), D689-D691, 2006
Minimum information requested in the annotation of biochemical models (MIRIAM)
NL Novère, A Finney, M Hucka, US Bhalla, F Campagne, J Collado-Vides, ...
Nature biotechnology 23 (12), 1509-1515, 2005
An auxin-driven polarized transport model for phyllotaxis
H Jönsson, MG Heisler, BE Shapiro, EM Meyerowitz, E Mjolsness
Proceedings of the national academy of sciences 103 (5), 1633-1638, 2006
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
M Hucka, A Finney, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ...
Systems biology 1 (1), 41-53, 2004
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem
H Jönsson, M Heisler, GV Reddy, V Agrawal, V Gor, BE Shapiro, ...
Bioinformatics 21 (Suppl 1), I232-I240, 2005
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
BE Shapiro, A Levchenko, EM Meyerowitz, BJ Wold, ED Mjolsness
Bioinformatics 19 (5), 677-678, 2003
Osmotic forces and gap junctions in spreading depression: a computational model
BE Shapiro
Journal of computational neuroscience 10, 99-120, 2001
Analysis of cell division patterns in the Arabidopsis shoot apical meristem
BE Shapiro, C Tobin, E Mjolsness, EM Meyerowitz
Proceedings of the National Academy of Sciences 112 (15), 4815-4820, 2015
MathSBML: a package for manipulating SBML-based biological models
BE Shapiro, M Hucka, A Finney, J Doyle
Bioinformatics 20 (16), 2829-2831, 2004
Reproducibility, fidelity, and discriminant validity of mRNA amplification for microarray analysis from primary hematopoietic cells
L Li, J Roden, BE Shapiro, BJ Wold, S Bhatia, SJ Forman, R Bhatia
The Journal of Molecular Diagnostics 7 (1), 48-56, 2005
An enzyme mechanism language for the mathematical modeling of metabolic pathways
CR Yang, BE Shapiro, ED Mjolsness, GW Hatfield
Bioinformatics 21 (6), 774-780, 2005
A quantitative analysis of single protein-ligand complex separation with the atomic force microscope
BE Shapiro, H Qian
Biophysical chemistry 67 (1-3), 211-219, 1997
A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12
CR Yang, BE Shapiro, S Hung, ED Mjolsness, GW Hatfield
Journal of Biological Chemistry 280 (12), 11224-11232, 2005
Developmental simulations with Cellerator
BE Shapiro, ED Mjolsness
Proceedings of the Second international Conference on systems Biology, 4-7, 2001
Signalling in multicellular models of plant development
H Jönsson, BE Shapiro, EM Meyerowitz, E Mjolsness
On growth, form and computers, 156-161, 2003
Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes
TS Najdi, CR Yang, BE Shapiro, GW Hatfield, ED Mjolsness
Journal of bioinformatics and computational biology 4 (02), 335-355, 2006
Using cellzilla for plant growth simulations at the cellular level
BE Shapiro, EM Meyerowitz, E Mjolsness
Frontiers in plant science 4, 408, 2013
Software infrastructure for effective communication and reuse of computational models
A Finney, M Hucka, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ...
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