| 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 | 3879 | 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 | 995 | 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 | 717 | 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 | 694 | 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 | 328 | 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 | 246 | 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 | 178 | 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 | 175 | 2003 |
| Osmotic forces and gap junctions in spreading depression: a computational model BE Shapiro Journal of computational neuroscience 10, 99-120, 2001 | 135 | 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 | 82 | 2015 |
| MathSBML: a package for manipulating SBML-based biological models BE Shapiro, M Hucka, A Finney, J Doyle Bioinformatics 20 (16), 2829-2831, 2004 | 73 | 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 | 65 | 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 | 53 | 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 | 48 | 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 | 46 | 2005 |
| Developmental simulations with Cellerator BE Shapiro, ED Mjolsness Proceedings of the Second international Conference on systems Biology, 4-7, 2001 | 41 | 2001 |
| 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 | 32 | 2006 |
| Signalling in multicellular models of plant development H Jönsson, BE Shapiro, EM Meyerowitz, E Mjolsness On growth, form and computers, 156-161, 2003 | 31 | 2003 |
| Using cellzilla for plant growth simulations at the cellular level BE Shapiro, EM Meyerowitz, E Mjolsness Frontiers in plant science 4, 408, 2013 | 29 | 2013 |
| Software infrastructure for effective communication and reuse of computational models A Finney, M Hucka, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ... | 28 | 2006 |
