Citing Cellerator and Related Packages

Citation for Cellzilla:
Shapiro BE, Meyerowitz E and Mjolsness E. Using Cellzilla for Plant Growth Simulations at the Cellular Level. (2013) Front. Plant Sci. 4:408 [doi: 10.3389/fpls.2013.00408]
Citation for kMech:
Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW. An enzyme mechanism language for the mathematical modeling of metabolic pathways. Bioinformatics 21(6): 774-780 (2005). [doi: 10.1093/bioinformatics/bti068 ]
Citation for MathSBML:
Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics 20(16):2829-2831 (2004) [doi: 10.1093/bioinformatics/bth271]
Citation for Cellerator:
Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED. Cellerator: extending a computer algebra systems to include biochemical arrows for signal transduction simulations. Bioinformatics 19(5):677-678 (2003) [doi: 10.1093/bioinformatics/btg042]

Selected Publications that Cite Cellerator

This list includes a sampling of papers from the literature that that cite Cellerator and Cellzilla as being used to complete their research. For further information please contact the authors directly.

Chang I, Baldi P. A Unifying Kinetic Framework for Modeling Oxidoreductase Catalyzed Bioenergetic Reactions (2013) Bioinformatics, 29(10):1299-1307 [DOI 10.1093/bioinformatics/btt140]
Costa, P.R., Acencio, M.L., and Lemke, N. Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation PLoS One. 2013; 8(2): e57328 [doi: 10.1371/journal.pone.0057328]
Ang Li, Meng Chen, Ting-Xin Jiang, Ping Wu, Qing Nie, Randall Widelitz, and Cheng-Ming Chuong, Shaping organs by a wingless-int/Notch/nonmuscle myosin module which orients feather bud elongation PNAS. 2013; 110:E1452-E1461. [doi:10.1073/pnas.1219813110]
Compani B, Su T, Chang I, Cheng I, Shah KH, Whisenant T, Dou Y, Bergmann A, Cheong R, Wold B, Bardwell L, Levchenko A, Paldi P, Mjolsness E. A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology. Adv. Exp. Medicine and Biology, 680(6):523-534 (2010) [DOI: 10.1007/978-1-4419-5913-3_58]
Pepke S, Kinzer-Ursem T, Mihalas M, Kennedy MB. A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II. PLOS Computational Biology 6(2):e1000675 (2010) [doi:10.1371/journal.pcbi.1000675]
Cui J, Kaandoop JA, Lloyd CA. Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli. BMC Systems Biology 2:89 (2008) [doi:10.1186/1752-0509-2-89]
Yang CR. An enzyme-centric approach for modelling non-linear biological complexity. BMC Systems Biology, 2:70 (2008) [doi: 10.1186/1752-0509-2-70]
Nadji TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. J. Bioinformatcs and Computational Biology 4(2):35-355 (2006).[DOI: 10.1142/S0219720006001862]
Gor V, Shapiro BE, Jonsson 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 (ed: N, Kolchanov, R. Hofestaedt, L. Milanesi), Springer (2005) [ISBN 8181283775]
Fernando CT, Rowe J. Hebbian learning in a simple gene circuit in. Proc. 9th Annual Conference on Genetic and Evolutionary Computing (GECCO), pp. 426. Full Paper at CiteSeer [http://dx.doi.org/10.1145/1276958.1277046]
Hicks MJ, Yang CR, Kotlajich MV, Hertel KJ. Linking Splicing to Pol II Transcription Stabilizes Pre-mRNAs and Influences Splicing Patterns. PLOS Biology 4(6):e147 (2006)[doi: 10.1371/journal.pbio.0040147]
Podkolodny NL, Podkolodnaya NN, Miginsky DS, Poplavsky AS, Likhoshvai VA, Compani B, Mjolsness E. An Integration of the Descriptions of Gene Networks and Their Models Presented in SIGMOID (Cellerator) and GENENET . In: Bioinformatics of Genome Regulation and Function, BGRS 2006, Volume 3, pp. 86-90
Cheng J, Scharenbroich L, Baldi P, Mjolsness E. Sigmoid: a software infrastructure for pathway bioinformatics and systems biology. IEEE Intelligent Systems 20(3):68-75 [DOI 10.1109/MIS.2005.51]
Cheong R, Bergmann A, Werner SL, Regal J, Hoffmann A, Levchenko A. Transient I-kappa-B Kinase Activity Mediates Temporal NF-kappa-B Dynamics in Response to a Wide Range of Tumor Necrosis Factor-alpha Doses J. Biol. Chem. 281(5):2945-2950 (2006). [doi: 10.1074/jbc.M510085200]
Hilioti ZA, Gallagher DA, Low-Nam ST, Ramaswamy P, Gajer P, Kingsbury TJ, Birchwood CJ, Levchenko A, Cunningham KW. GSK-3 kinases enhance calcineurin signaling by phosphorylation of RCNs . Genes. Dev. 18(1):35-47 (2003) [doi: 10.1101/gad.1159204]
Shapiro BE, Levchenko A, Mjolsness E Automatic Model Generation for Signal Transduction with Applications to MAP-Kinase Pathways in Foundations of Systems Biology (ed: H. Kitano), MIT Press, pp. 145-162 (2002) [ISBN 0-262-11266-3]

Selected Posters

(ISMB-2007/Vienna - 2.2 MB pdf). Mathematica Platforms for Modeling in Systems Biology: Recent Developments in MathSBML and Cellerator, Shapiro BE, Lu J, Hucka M, Mjolsness E.
(ICSB-2006/Yokohama - 2.9 MB png). Systems Biollogy Software Support in Mathematica: Recent Developments in Cellerator, Shapiro BE, Vorobyov A, Murakami JG, Mjolsness ED.
(ICSB-2004/Heidelberg - 2.4 MB pdf). MathSBML: A Mathematica Package for Systems Biology, Shapiro BE, Hucka M, Finney A.
(PSB-2004/Hawaii - 1.9 MB pdf). MathSBML and Systems Biology Simulations, Shapiro BE, Hucka M, Finney A.
(ICSB-2001/Pasadena - 2.4 MB pdf). Developmental Simulations with Cellerator, Shapiro BE, Mjolsness ED.
(SIAM-2001/San Diego - 1.2 MB pdf). Automatic Equation Generation for Signal Transduction Modeling, Shapiro BE, Levchenko A, Mjolsness E.