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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.
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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.
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., 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.
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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.