Biblio

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T
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.
R
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.
E. Erdem, Lifschitz, V., Nakhleh, L., and Ringe, D., Reconstructing the Evolutionary History of Indo-European Languages using Answer Set Programming, in Proceedings of the Fifth International Symposium on Practical Aspects of Declarative Languages (PADL 2003), 2003, vol. 2562, pp. 160-176.
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.
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.
P
C. Coarfa, Dotsenko, Y., Mellor-Crummey, J., Nakhleh, L., and Roshan, U., PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction, in Proceedigns of the First IEEE Workshop on High Performance Computing in Medicine and Biology, 2005, vol. 2, pp. 346-350.
Y. Dotsenko, Coarfa, C., Nakhleh, L., Mellor-Crummey, J., and Roshan, U., PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction, International Journal on Bioinformatics Research and Applications, vol. 2, pp. 407-419, 2006.
C. Than, Ruths, D., and Nakhleh, L., PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships, BMC Bioinformatics, vol. 9, p. 322, 2008.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., The Performance of Phylogenetic Methods on Trees of Bounded Diameter, in First International Workshop on Algorithms in Bioinformatics (WABI 01), 2001, vol. Lecture Notes in Computer Science 2149, pp. 214–226.
L. Nakhleh, Ringe, D., and Warnow, T., Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages, LANGUAGE, Journal of the Linguistic Society of America, vol. 81, pp. 382-420, 2005.
Z. Du, Stamatakis, A., Lin, F., Roshan, U., and Nakhleh, L., Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood, in Proceedings of the 2005 International Conference on High Performance Computing and Communications, 2005, vol. 2, pp. 346-350.

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