Biblio

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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.
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, 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.
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)
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., and Ram, P. T., Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle, BMC Systems Biology, vol. 2, p. 76, 2008.