Biblio

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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, 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 and Nakhleh, L., Boosting forward-time population genetic simulators through genotype compression, BMC Bioinformatics, vol. 14, p. 192, 2013.PDF icon RuthsNakhleh-BMCBioinfo13.pdf (680.55 KB)
D. Ruths and Nakhleh, L., Techniques for Assessing Phylogenetic Branch Support: A Performance Study, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 187-196.
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.
T. Ruths and Nakhleh, L., Neutral forces acting on intragenomic variability shape the E. coli regulatory network topology, Proceedings of the National Academy of Sciences, vol. 110, no. 19, pp. 7754-7759, 2013.PDF icon RuthsNakhleh-PNAS13.pdf (2.57 MB)
D. Ruths and Nakhleh, L., RECOMP: A Parsimony-based Method for Detecting Recombination, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 59-68.
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 and Nakhleh, L., ncDNA and drift drive binding site accumulation, BMC Evolutionary Biology, vol. 12, p. 159, 2012.PDF icon RuthsNakhleh-BMCEvolBiol2012.pdf (659.08 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 and Nakhleh, L., Recombination and phylogeny: effects and detection, International Journal on Bioinformatics Research and Applications, vol. 1, pp. 202-212, 2005.
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.