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Y. Lu, Muller, M., Smith, D., Dutta, B., Mourov, K., Iadevaia, S., Ruths, D., Tseng, J. - T., Yu, S., Yu, Q., Nakhleh, L., Balazsi, G., Donnelly, J., Schurdak, M., Morgan-Lappe, S., Fesik, S., Ram, P. T., and Mills, G. B., Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling, Oncogene, vol. 30, pp. 4567-4577, 2011.PDF icon Oncogene2011.pdf (905.3 KB)
D. Ruths and Nakhleh, L., Deriving predictive models of signaling network dynamics from qualitative experimental data, in Proceedings of the 9th Annual International Conference on Computational Systems Biology, 2010.PDF icon RuthsNakhleh-CSB2010.pdf (548.82 KB)
T. Ruths, Ruths, D., and Nakhleh, L., GS2: An efficiently computable measure of GO-based similarity of gene sets, Bioinformatics, vol. 25, pp. 1178-1184, 2009.
D. Ruths, Muller, M., Tseng, J. T., Nakhleh, L., and Ram, P. T., The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizing the Dynamics of Cell-specific Signaling Networks, PLoS Computational Biology, vol. 4, p. e1000005, 2008.
D. Ruths, Nakhleh, L., and Ram, P. T., Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle, BMC Systems Biology, vol. 2, p. 76, 2008.
D. Ruths, Tseng, J. T., Nakhleh, L., and Ram, P. T., De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis, in Proceedings of the RECOMB Satellite Workshop on Systems Biology and Proteomics, 2007, vol. 4205, pp. 108-118.
D. Ruths, Nakhleh, L., Iyengar, M. S., Reddy, S. A. G., and Ram, P. T., Graph-theoretic Hypothesis Generation in Biological Signaling Networks, Journal of Computational Biology, vol. 13, pp. 1546-1557, 2006.