Biblio

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2010
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)
2009
L. Nakhleh, Ruths, D., and Innan, H., Gene trees, species trees, and species networks, in Meta-analysis and Combining Information in Genetics, R. Guerra and Goldstein, D., Eds. Chapman & Hall, CRC Press, 2009, pp. 275-293.
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.
2006
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.
C. Than, Ruths, D., Innan, H., and Nakhleh, L., Identifiability issues in phylogeny-based detection of horizontal gene transfer, in Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop, 2006, vol. 4205, pp. 215-219.
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., Techniques for Assessing Phylogenetic Branch Support: A Performance Study, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 187-196.
2005
D. Ruths and Nakhleh, L., Recombination and phylogeny: effects and detection, International Journal on Bioinformatics Research and Applications, vol. 1, pp. 202-212, 2005.
L. Nakhleh, Ruths, D., and Wang, L. S., RIATA-HGT: A Fast and accurate heuristic for reconstrucing horizontal gene transfer, in Proceedings of the Eleventh International Computing and Combinatorics Conference (COCOON 05), 2005, vol. 3595, pp. 84-93.