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Papers in Journals
  1. Shapiro BE, Mjolsness E (2015) Pycellerator: an arrow-based reaction-like modelling language for biological simulations. Bioinformatics Advance Access, 31 Oct. 2015 (doi: 10.1093/bioinformatics/btv596).
  2. Shapiro BE, Tobin C, Mjolsness ED, Meyerowitz ED (2015) Analysis of Cell Division Patterns in the Arabadopsis Shoot Apical Meristem. PNAS, 112(15):4815-4820. doi: 10.1073/pnas.1502588112
  3. Shapiro BE, Meyerowitz EM, Mjolsness ED (2013) Using Cellzilla for Plant Growth Simulations at the Cellular Level Front. Plant Sci. 4:408. doi: 10.3389/fpls.2013.00408
  4. Nikolaev SV, Zubairova US, Penenko AV, Mjolsness BE, Shapiro BE, Kolchanov NA (2013) Модель регуляции структуры ниши стволовых клеток в апикальной меристеме побега Arabidopsis thaliana [Model of structure regulation of stem cell niche in shoot apical meristem of Arabidopsis thaliana] Doklady Akademii Nauk, 453 (3): 336–338, DOI: 10.7868/S0869565213280268
  5. Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED (2006) Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes. J. Bioinform. Comput. Biol. 94 (335) [ DOI: 10.1142/S0219720006001862 ]
  6. Jönsson H, Heisler M, Shapiro BE, Meyerowitz EM, Mjolsness ED (2006) An auxin driven polarized transport model for phyllotaxis. Proc. Natl. Acad. Sci, U.S.A. 103(5) 1644-1638 [doi: 10.1073/pnas.0509839103]
  7. Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M (2006) BioModels, database of curated quantitative kinetics models. Nucleic Acids Research 34:D689-D691 [doi: 10.1093/nar/gkj092].
  8. Le Novère, L., Finney, A., Hucka, M., Bhalla, U., Campagne, F., Collado-Vides, J., Crampin, E., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B, Snoep, J., Spence, H., and Wanner, B. (2005) Minimal information requested in the annotation of models (MIRIAM). Nature Biotechnology, 23(12):1509-1515. [doi:10.1038/nbt1156]
  9. Jönsson H, Heisler M, Reddy GV, Agrawal V, Gor V, Shapiro BE, Mjolsness E, Meyerowitz EM (2005) Modeling the organization of the WUSCHELexpression domain in the shoot apical meristem Bioinformatics, 21(S1);i232-i240; doi: 10.1093/bioinformatics/bti1036.
  10. Yang CR, Shapiro BE, Hung S, Mjolsness ED (2005) A Mathematical Model for the Branched Chain Amino Acid Biosynthetic Pathways of Escherichia coli K12. Journal of Biological Chemistry, 280(12):11224-11232.
  11. Li L, Roden J, Shapiro BE, Wold BJ, Forman SJ, Bhatia R (2004) Reproducibility, fidelity and discriminant validity of mRNA amplification for microarray analysis of primary hematiopoietic cells. Journal of Molecular Diagnostics, 7(1):48-56
  12. Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW (2005) An enzyme mechanism language for the mathematical modeling of biochemical pathways. Bioinformatics,21(6):774-780, doi:10.1093/bioinformatics/bti068.
  13. M. Hucka, A. Finney, B.J. Bornstein, S.M. Keating, B.E. Shapiro, J. Matthews, B.L. Kovitz, M.J. Schilstra, A. Funahashi, J.C. Doyle and H. Kitano (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project, IEE Systems Biology, 1:41-53.
  14. Shapiro BE, Hucka M, Finney A, Doyle M (2004) MathSBML: A package for manipulating SBML based biological models. Bioinformatics, (Advance Access published online 15 April 2004) DOI: 10.1093/bioinformatics/bth271.
  15. Shapiro BE, Levchenko A, Wold BJ, Meyerowitz EM, Mjolsness ED (2003) Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction modeling. Bioinformatics 19(5): 677-678
  16. 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 Novere N, Loew LM, Lucio D, P. Mendes P, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu S, Spence HD, Stelling J, Takahashi K, M. Tomita M, Wagner J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 (4):513-523
  17. Shapiro BE (2001) Gap Junctions and Osmosis in Spreading Depression: A Computational Model, Journal of Computational Neuroscience 10(1):99-120.
  18. Qian H, Shapiro BE (1999) Graphical Method for Force Analysis: Macromolecular Mechanics with Atomic Force Microscopy. Proteins: Structure, Function and Genetics, 37:576-581.
  19. Frauenholz RB, Bhat RS, Shapiro BE, Leavitt RK (1998) The TOPEX/Poseidon Operational Orbit. Journal of Spacecraft and Rockets. 35:212-224.
  20. Shapiro BE, Qian H (1998) Hysteresis in Force Probe Microscopy: A Dynamical Systems Perspective. Journal of Theoretical Biology. 194:551-559.
  21. Shapiro BE, Qian H (1997) A Quantitative Analysis of Single Protein-Ligand Complex Separation with the Atomic Force Microscope. Biophysical Chemistry. 67:211-219
  22. Shapiro BE (1988) The GEOSAT Orbit Adjust. Journal of the Astronautical Sciences. 36:407-424.
 
Book Chapters
  1. Shapiro BE, Jönsson H, Sahlin P, Heisler M, Roeder A, Bulr M, Meyerowitz EM, Mjolsness ED.(2011) Tessellations and Pattern Formation in Plant Growth and Development. In Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, ed. van de Weygaert R, Vegter G, Ritzerveld J, Icke V. Springer-Verlag (accepted by editor) [archiv preprint].
  2. Shapiro BE, Finney A, Hucka A, Bornstein B, Funahashi A, Jouraku A, Keating SM, Le Novereère N, Matthews J, Schilstra MJ (2006) SBML Models and MathSBML. Chapter 39 of Introduction to Systems Biology, ed. S. Choi, Humana Press.
  3. Gor V, Shapiro BE, Jönsson H, Heisler M, Reddy GV, Meyerowitz EM, Mjolsness E (2006) A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project, in Bioinformatics of Genome Regulation and Structure II, ed. N Kolchanov, R Hofestaedt, L Milanesi, Springer.
  4. Mjolsness E, Jönnson H, Shapiro BE, Meyerowitz EM (2004) Modeling plant development with gene regulation networks including signaling and cell division, in Bioinformatics of Genome Regulation and Structure, ed. N. A. Kolchanov, Kluwer Publications, pp. 311-318.
  5. Jönsson H, Shapiro BE, Meyerowitz EM, Mjolsness E (2003) Signaling in Multicellular Models of Plant Development, in On Growth, Form, and Computers, ed. Bentley P and Kumar S, Academic Press, pages 156-161.
  6. Shapiro BE, Levchenko A, Mjolsness E (2002) Automatic Model Generation for Signal Transduction with Applications to Map Kinase Pathways (in: Foundations of Systems Biology, H. Kitano, ed, MIT Press, pages 145-162) ISBN 0-262-11266-3
  7. Bhat RS, Shapiro BE, Frauenholz RB, Leavitt RK (1998) TOPEX/Poseidon Orbit Maintenance for the First Five Years. Advances in the Astronautical Sciences. 100(2): 973-988
  8. Shapiro BE (1995) Phase Plane Analysis and Frozen Orbit for TOPEX/Poseidon. Advances in the Astronautical Sciences. 91(1): 853-872.
  9. Frauenholz R, Bhat RS, Shapiro BE (1995) Leavitt RK, An Analysis of the Topex-Poseidon Observational Orbital, Observed Variation and Why, Advances in the Astronautical Sciences.
  10. Shapiro BE, Bhat R (1994) The Use of Anomalous Satellite Fixed Forces to Control the TOPEX/Poseidon Ground Track. Advances in the Astronautical Sciences. 87(2): 799-812
  11. Frauenholz RB, Hamilton TW, Shapiro BE, Bhat RS (1993) The role of anomalous satellite-fixed accelerations in Topex/Poseidon orbit maintenance. Advances in the Astronautical Sciences, 85(1):83-102.
  12. Bhat RS, Shapiro BE, Frauenholz RB (1993) TOPEX/Poseidon Orbit Acquisition Maneuver Sequence. Advances in the Astronautical Sciences. 85(1): 103-122
  13. Frauenholz RB, Shapiro BE (1991) The Role of Predicted Solar Activity in the TOPEX/Poseidon Orbit Maintenance Maneuver Design. Advances in the Astronautical Sciences. 76(2):1151-1170
 
Papers Presented at Conferences and Meetings
  1. Nikolaev SV, Zubariova US, Mjolsness E, Smal P, Shapiro B, Solchanov NA (2010) A reaction diffusion model of SAM spatial structure regulation. 3rd International conference on Mathematical Biology and Bioinformatics, Moscow (Russia).
  2. Shapiro BE, Heisler M, Tobin C, Cunha A, Davis A, Mjolsness ED, Meyerowitz EM (2010) Using Geometric Markers to Predict the Cell Division Plane in Meristem Cells. Sixth International Conference on Functional-Structural Plant Mechanics, Davis CA (USA).
  3. Cunha A, Roeder A, Shapiro B, Tarr P, Tobin C, Meyerowitz E (2010) Cell Image Analysis as a Basis for Understanding Plant Growth, Bioimage Informatics. Pittsburgh, PA (USA)
  4. Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. (2005) Application of a Generalized MWC Model for the Mathematical Simulation of Pathways Regulated by Allosteric Enzymes. IEEE Computational Systmes Bioinformatics Conference.
  5. Gor V, Shapiro BE, Jönsson H, Heisler M, Venugopala Reddy G, Meyerowitz EM, Mjolsness E (2004) A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project. Presented at the 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS-2004), Novosibirsk, Russia, July 2004.
  6. Mjolsness E, Shapiro BE, Gor V, Jönnson H (2002) Gene regulation networks with signalling and cell division in developmental simulations, Second Joint Meeting of the IEEE Engineering in Medicine and Biology Society (IEEE/EMBS) and the Biomedical Engineering Society (BMES), Houston TX, USA, Oct 23-26, 2002.
  7. Mjolsness E, Jönnson H, Shapiro BE, Meyerowitz EM (2002) Modeling plant development with gene regulation networks including signaling and cell division, paper presented at the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), Novosibirsk, Russia, July 14-20, 2002.
  8. Shapiro BE, Mjolsness ED (2001) Developmental Simulations with Cellerator, paper presented at the Second International Conference on Systems Biology, Pasadena, CA, Novemeber 2001.
  9. Shapiro BE, Levchenko A, Mjolsness E (2000) Automatic Model Generation for Signal Transduction with Applications to Map Kinase Pathways. paper presented at the First International Conference on Systems Biology, Tokyo, Japan, December 2000.
  10. Shapiro BE (1995) Phase plane analysis and observed frozen orbit for the Topex/Poseidon mission. Presented at the Sixth International Conference of Pacific Basin Societies, Marina del Rey, CA, USA, December 6-8, 1995. Reprinted in Advances in the Astronautical Sciences, Volume 91, pages 853-872.
  11. Frauenholz RS, Bhat RS, Shapiro BE, Leavitt RK (1995) An analysis of the TOPEX/Poseidon operational orbit: observed variation and why, AAS/AIAA Astrodynamics Specialist Conference, Halifax, Nova Scotia, Canada, August 14-17, 1995
  12. Shapiro BE, Bhat RS, Frauenholz RB (1994) Using anomalous along-track forces to control the Topex/Poseidon ground track. AAS/AIAA Spaceflight Mechanics Meeting, Cocoa Beach, FL, USA, February 14-16, 1994. Reprinted in Advances in the Astronautical Sciences, volume 87, pages 799-812
  13. Bhat RS, Shapiro BE, Frauenholz RB (1993) Topex/Poseidon orbit acquisition maneuver sequence. AAS/AIAA Astrodynamics Specialist Conference, Victoria, BC, Canada, August 16-19, 1993. Reprinted in Advances in the Astronautical Sciences, Volume 85, pages 103-122.
  14. Frauenholz RB, Hamilton TW, Shapiro BE, Bhat RS (1993) The role of anomalous satellite-fixed accelerations in Topex/Poseidon orbit maintenance. AAS/AIAA Astrodynamics Specialist Conference, Victoria, BC, Canada, August 16-19, 1993. Reprinted in Advances in the Astronautical Sciences, Volume 85, pages 83-102.
  15. Shapiro BE, Bhat RS (1993) GTARG - The Topex/Poseidon ground track maintenance maneuver targeting program. AIAA/AHS/ASEE Aerospace Design Conference. Irvine, CA, USA, February 16-19, 1993. AIAA Paper 98-1129.
  16. Frauenholz RB, Shapiro BE (1991) The role of predicted solar activity in Topex/Poseidon orbit maintenance maneuver design. AAS/AIAA Astrodynamics Specialist Conference, Durango, CO, USA, August 19-22, 1991. Reprinted in Advances in the Astronautical Sciences, volume 76, pp. 1151-1170.
  17. Shapiro BE, Pino A (1988) Maintenance of an exact repeat orbit - the Geosat ERM. AIAA/AAS Astrodynamics Conference, Minneapolis, MN, USA, August 15-17, 1988. AIAA Paper 88-4301-CP.
 
Posters Presented at Conferences and Meetings
  1. Jonsson A, Chickarmane V, Gordon S, Heisler M, Krupinski P, Pontus M, Meyerowitz E, Mjolsness E, Roeder A, Sahlin P, Shapiro B (2008) The Computable Plant. Arena at 9th International Conference on Systems Biology, Gothenburg, (SWEDEN)
  2. Schwarz EM, Mortazavi A, Kuntz SG, Saldanha AJ, Shapiro BE, Wold BJ, Sternberg PW. (2007) Cis-regulatory analysis of four Caenorhabditis genomes. 16th International C. elegans Meeting, Los Angeles, CA (USA).
  3. Shapiro BE, Lu J, Hucka M, Mjolsness ED (2007) Recent Developments in MathSBML and and Cellerator. 8th International Conference on Systems Biology (ICSB-2007) Long Beach, CA (USA)
  4. Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED (2007) Enzyme-mechanism models and simulations of central metabolism pathways and amino acid biosynthesis in Escherichia coli. (2007) 8th International Conference on Systems Biology (ICSB-2007) Long Beach, CA (USA).
  5. Li C, Donizelli M, Le Novere N, Dharuri H, He E, Li L, Shapiro BE, Stefan M, Laibe C, Tolle D, Schiappa R, Hucka M. (2007) Biomodels Database, a curated and annotated resource of published quantitative kinetic models. 8th International Conference on Systems Biology (ICSB-2007) Long Beach, CA (USA)
  6. Shapiro BE, Hucka M, Lu J, Mjolsness, ED (2007) Mathematica Platforms for Systems Biology (2007). 15th International Conference of Intelligent Systems in Molecular Biology (ISMB-2007), Vienna (AUSTRIA)
  7. Jonsson H, Heisler M, Shapiro BE, Meyerowitz EM, Mjolsness E (2006) An auxin transport model for regulation of plant organ initiation. 7th International Conference on Systems Biology (ICSB-2006), Yokohama (Japan)
  8. Bornstein B, Keating S, Shapiro BE, Murakami J, Hucka M (2006) Recent Updates to libSBML, MathSBML, SBML- Toolbox, and the SBML.org Online Validator (2006) 7th International Conference on Systems Biology (ICSB-2006), Yokohama (Japan).
  9. Hucka M, Finney A, Bornstein B, Shapiro B, Keating S, Schilstra M, Funahashi A, Joukaru A Matthews J, Kovitz B (2006) Open Source Software from the SBML Team (2006 )Pacific Symposium on Biocomputing, Wailea, HI (USA).
  10. Roden J, Hernandez G, Williams B, Kuntz DS, Mortazevi A, King B, Trout D, Wold B, Shapiro BE. (2006) A genome-wide study of cis-regulation within the microgravity-induced muscle atrophy transciptome. Pacific Symposium on Biocomputing, Wailea, HI, (USA)
  11. Hucka M, Finney A, Bornstein B, Shapiro B, Keating S, Schilstra M, Funahashi A, Joukaru A Matthews J, Kovitz B (2005) Software from the SBML Team: LibSBML, MathSBML, SBMLToolbox, CellML2SBML, KEGG2SBML, SBML Test Suite and the Online Tools. Fifth international Confrence on System Biology (ICSB-2005), Boston, MA, USA Oct. 19-24, 2005.
  12. Shapiro BE, Agrawal V, Gor V, Heisler M, Jonsson H, Meyerowitz EM, Mjolsness E, Reddy VG. A Computational Modeling Framework for the Arabidopsis Shoot Apical Meristem. Annual Meeting of the American Society of Plant Biologists, July 16-20, 2005, Seattle, WA, USA.
  13. Shapiro BE, Hucka M, Finney A, SBML Model-Based Simulation with MathSBML, Poster presented at the 13th International Conference of Intelligent Systems in Molecular Biology (ISMB)/Annual Meeting of the International Society for Computational Biology (ISCB), Detroit MI, USA, June 2005.
  14. Agrawal V, Gor V, Heisler M, Jönnson H, Meyerowitz EM, Mjolsness E, Reddy GV, Sadovsky A, Shapiro BE, Developmental Modeling of the Arabidopsis Shoot Apical Meristem. 44th Annual Meeting of the American Society for Cell Biology, Washington, DC, USA, Dec 4-8, 2004.
  15. Shapiro BE, Hucka M, Finney A (2004) MathSBML: A Mathematica Package for Systems Biology, 5th International Conference on Systems Biology, Heidelberg, Germany, October 2004.
  16. Mjolsness E, Shapiro B, Gor V, Jönsson H, Reddy GV, Heisler M, Meyerowitz EM (2004) The Computable Plant: A Software Architecture for Developmental Modeling in Plants, Pacific Symposium on Biocomputing (PSB-2004) Big Island, Hawai'i, USA.
  17. Shapiro BE, Hucka M, Finney A MathSBML and Systems Biology Simulations, Pacific Symposium on Biocomputing (PSB-2004) Big Island, Hawai'i, USA.
  18. Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, Ben Bornstein, Bruce Shapiro, Maria Schilstra, Ben Kovitz, Joanne Matthews, Sarah Keating, Akira Funahashi, John Doyle, Hiroaki Kitano (2003) The Systems Biology Markup Language (SBML), Intelligent Systems for Molecular Biology (ISMB-2003), Brisbane, Australia.
  19. Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, Ben Bornstein, Bruce Shapiro, Maria Schilstra, Ben Kovitz, Joanne Matthews, Sarah Keating, Akira Funahashi, John Doyle, Hiroaki Kitano (2003), The Systems Biology Markup Language. Presented at the First IECA Conference on Systems Biology of E. Coli, Tsuruoaka, Japan (2003).
  20. Jonsson HJ, Shapiro BE, Meyerowitz EM, Mjolsness ED (2002) Signaling in Multicellular Models of Plant Development. Third International Conference on Systems Biology (ICSB-2002), Stockholm Sweden, November 2002.
  21. Finney A, Hucka M, Sauro H, Bolouri H, Funahashi A, Bornstein B, Kovitz B, Matthews J, Shapiro B, Keating S, Doyle J, Kitano H (2002) The Systems Biology Workbench (SBW) Version 1.0: Frameworks and Modules Third International Conference on Systems Biology, Stockholm, Sweden (ICSB-2002), November 2002.
  22. Shapiro BE, Mjolsness ED (2001) Developmental Simulations with Cellerator, Second International Conference on Systems Biology, (ISCB-2001) Pasadena, CA, December, 2001.
  23. Shapiro BE, Levchenko A, Mjolsness ED (2001) Automatic Equation Generation fo Signal Transduction Modeling 2001 SIAM Annual Meeting, San Diego, CA, USA, July 2001.
  24. Shapiro BE (1999) Leao's Spreading Depression and Gap Junctions: An Electrodiffusion Model of the DC-Voltage Shift, Ionic Movement, and Osmotic Volume Changes. Society of Neuroscience 29th Annual Meeting, Miami Beach, FL, USA, October 23-28, 1999, Society of Neuroscience Abstracts. 25:128.6.
  25. Shapiro BE (1997) Macromolecular Separation with the Atomic Force Microscope: A Dynamical Systems Perspective. Society for Mathematical Biology Annual Meeting, Raleigh, North Carolina, August 1997.
 
Citations in NASA Tech Briefs
  1. Software for Modeling Biochemical Reactions(Cellerator),26(7):34, July 2002,NPO-21122.
  2. Analysis of the Orbit of the Topex/Poseidon Satellite, 20(9):100, Sept. 1996, NPO-19853.
  3. Computing Maneuvers for a Repeating Ground Track (GTARG), 18(12):61, Dec. 1994, NPO-19257. GTARG Software program released to the public domain.
 
Presentations
  1. Quantitative Biology Analyzed by Mathematical Models, invited guest faculty at Johan Radon Institute for Computational and Applied Mathematics (RICAM), (2007) Linz (AUSTRIA)
  2. Tessellations in the Sciences, invited guest faculty, Lorentz Center (2006), Leiden University, Leiden (The Netherlands).
  3. Modeling Plant Growth: The Shoot Apical Meristem, presented at California State University, Los Angeles, USA, Aug 2005.
  4. A Computational Modeling Framework for the Arabidopsis Shoot Apical Meristem, presented at the annual meeting of the American Society for Plant Biology, July 16-20, 2005, Seattle, WA, USA.
  5. Developmental Model of the Arabidopsis Shoot Apical Meristem by the Computable Plant Project, invited Keynote Address, 35th Biological Systems Simulation Conference April 19-21, 2005, Phoenix, AZ, USA.
  6. The Computable Plant. Presented at the 2004 SIAM Conference on Life Sciences, Portland, Oregon, USA, July 11-14, 2004.
    View Conference Web Site.
  7. Supplementary Material for: Complex Systems in Computer Science in Biology, Rovereto (TN) Italy, 2004
  8. Understanding the Genome: How Close are we to Star Trek Medicine? Presented at JPL; CSU, Fullerton; and the University of Souther California.
  9. Helping Mathematics Students Develop Information Competency, MAA Section NExT, 3/8/03 (powerpoint)
  10. Tidbits from the Sciences: Examples for Calculus and Differential Equations , MAA Section NExT, 3/8/03 (powerpoint)
  11. Cellerator: A System for Simulating Biochemical Reaction Networks (powerpoint)
  12. Osmosis and Gap Junctions in Spreading Depression: A Mathematical Model (powerpoint)