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Cellerator
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Publications
  • (2001) Shapiro, BE and Mjolsness, ED "Developmental Simulations with Cellerator," Proceedings of the Second International Conference on Systems Biology, pp. 342-351.

  • (2001) Shapiro, BE, Levchenko, A, and Mjolsness, ED, "Automatic Model Generation with Applications to MAP-Kinase Pathways," in Foundations of Systems Biology, ed. H. Kitano, MIT Press.

  • (2002)Shapiro, BE, Levchenko, A, Meyerowitz, EM, Wold, BJ, and Mjolsness, ED. "Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations, Bioinformatics, 19(5): 677-678.

  • (2002)Mjolsness E, Jönnson H, Shapiro BE, Meyerowitz EM "Modeling plant development with gene regulation networks including signaling and cell division," Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2002), Novosibirsk, Russia, July 14-20.

  • (2002)Mjolsness E, Shapiro BE, Gor V, Jönnson H "Gene regulation networks with signalling and cell division in developmental simulations," Proceedings of the 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.

  • (2002)Jönnson H, Shapiro BE, Meywerowitz, EM, Mjolsness E, "Signalling in multicellular models of plant development," Third International Conference on Systems Biology, Stockholm, Sweden, Dec. 2002.

  • (2003)Hilioti, Z., Gallagher, D.A., Low-Nam, S. T., Ramaswamy, P., Gajer, P., Kingsbury, T.J., Birchwood, C.J., Levchenko, A., and Cunningham, K.W. (2004) "GSK-3 Kinases Enhance Calcineurin Signaling by Phosphorylation of RCNs," Genes and Development 18: 35-47.

  • (2005)Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW. An enzyme mechanism language for the mathematical modeling of biochemical pathways. Bioinformatics,21(6):774-780,

  • (2005)Yang CR, Shapiro BE, Hung S, Mjolsness ED. A Mathematical Model for the Branched Chain Amino Acid Biosynthetic Pathways of Escherichia coli K12.

  • (2006)Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. The Generalized Monod, Wyman, Changeux Model for Mathematical Modeling of Metabolic Enzymes with Allosteric Regulation, Journal of Bioinformatics and Computational Biology (in press).

  • (2006) Gor V, Shapiro BE, Jönnson H, Heisler M, Reddy GV, Meyerowitz EM, Mjolsness E. 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.

  • (2006) Shapiro BE, Voroboyov A, Murakami J, Mjolsness E. New Developments in Cellerator. Poster presented at the International Conference on Systems Biology, Yokohama, Japan, October, 2006.

Citations (Publications that Cite Cellerator)
  • Kim JS, Yun H, Kim HU, et al., Resources for systems biology research JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY 16 (6): 832-848 JUN 2006
  • Hicks MJ, Yang CR, Kotlajich MV, et al., Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns PLOS BIOLOGY 4 (6): 943-951 JUN 2006
  • Sarai N, Matsuoka S, Noma A, simBio: A Java package for the development of detailed cell models PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 90 (1-3): 360-377 JAN-APR 2006
  • Cheong R, Bergmann A, Werner SL, et al., Transient I kappa B kinase activity mediates temporal NF-kappa B dynamics in response to a wide range of tumor necrosis factor-alpha doses JOURNAL OF BIOLOGICAL CHEMISTRY 281 (5): 2945-2950 FEB 3 2006
  • Chabrier-Rivier N, Fages F, Soliman S, The biochemical abstract machine BIOCHAM LECTURE NOTES IN COMPUTER SCIENCE 3082: 172-191 2005
  • Soliman S, Fages F, CMBSlib: A library for comparing formalisms and models of biological systems LECTURE NOTES IN COMPUTER SCIENCE 3082: 231-235 2005
  • Uhrmacher AM, Degenring D, Zeigler B, Discrete event multi-level models for systems biology LECTURE NOTES IN COMPUTER SCIENCE : 66-89 2005
  • Cheng JL, Scharenbroich L, Baldi P, et al., Sigmoid: A software infrastructure for pathway bioinformatics and systems biology IEEE INTELLIGENT SYSTEMS 20 (3): 68-75 MAY-JUN 2005
  • Li WJ, Kurata H, A grid layout algorithm for automatic drawing of biochemical networks BIOINFORMATICS 21 (9): 2036-2042 MAY 1 2005
  • Yang CR, Shapiro BE, Hung SP, et al., A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (12): 11224-11232 MAR 25 2005
  • Faeder JR, Blinov ML, Goldstein B, et al., Rule-based modeling of biochemical networks COMPLEXITY 10 (4): 22-41 MAR-APR 2005
  • Yang CR, Shapiro BE, Mjolsness ED, et al., An enzyme mechanism language for the mathematical modeling of metabolic pathways BIOINFORMATICS 21 (6): 774-780 MAR 15 2005
  • Blinov ML, Faeder JR, Goldstein B, et al., BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains BIOINFORMATICS 20 (17): 3289-3291 NOV 22 2004
  • Shapiro BE, Hucka M, Finney A, et al., MathSBML: a package for manipulating SBML-based biological models BIOINFORMATICS 20 (16): 2829-2831 NOV 1 2004
  • Reddy GV, Heisler MG, Ehrhardt DW, et al., Real-time lineage analysis reveals oriented cell divisions associated with morphogenesis at the shoot apex of Arabidopsis thaliana DEVELOPMENT 131 (17): 4225-4237 SEP 2004
  • Provart NJ, McCourt P, Systems approaches to understanding cell signaling and gene regulation - Commentary, CURRENT OPINION IN PLANT BIOLOGY 7 (5): 605-609 OCT 2004
  • Sauro HM, Kholodenko BN, Quantitative analysis of signaling networks, PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 86 (1): 5-43 SEP 2004
  • You LC, Toward computational systems biology , CELL BIOCHEMISTRY AND BIOPHYSICS 40 (2): 167-184 2004
Last Updated 1 December 2006