Biblio

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L. Nakhleh, Warnow, T., and Linder, C. R., “Reconstructing reticulate evolution in species–theory and practice”, in Proc.\ 8th Ann.İnt’l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB04}), 2004, pp. 337–346.
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, 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.
L. Nakhleh, “Computational approaches to species phylogeny inference and gene tree reconciliation”, Trends in Ecology and Evolution, vol. 28, no. 12, pp. 719-728, 2013.PDF icon TREE-Nakhleh13.pdf (559.43 KB)
L. Nakhleh, Warnow, T., Linder, C. R., and John, S. K., “Reconstructing reticulate evolution in species–theory and practice”, in Journal of Computational Biology, 2005, vol. 12(6-7), pp. 796-811.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., “Designing Fast Converging Phylogenetic Methods”, Bioinformatics, vol. 17, pp. S190–S198, 2001.
L. Nakhleh, Sun, J., Warnow, T., Linder, R., Moret, B. M. E., and Tholse, A., “Towards the development of tools for evaluating phylogenetic network reconstruction methods”, in Proc.\ 8th Pacific Symp. on Biocomputing ({PSB03}), 2003, pp. 315–326.
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.
L. Nakhleh, “A metric on the space of reduced phylogenetic networks”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, pp. 218-222, 2010.PDF icon tcbb-Metric.pdf (287.01 KB)
L. Nakhleh, Roshan, U., Vawter, L., and Warnow, T., “Estimating the Deviation from a Molecular Clock”, in Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI 02), Rome, Italy, 2002, vol. 2452, pp. 287-299.
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H. J. Park, Jin, G., and Nakhleh, L., “Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees”, Proceedings of the 9th Annual International Conference on Computational Systems Biology. pp. 114-123, 2010.PDF icon ParkEtAl-CSB2010.pdf (946.56 KB)
H. J. Park, Jin, G., and Nakhleh, L., “Bootstrap-based support of HGT inferred by maximum parsimony”, BMC Evolutionary Biology, vol. 10, p. 131, 2010.PDF icon BMCEvolBiol2010.pdf (1.18 MB)
H. J. Park and Nakhleh, L., “MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees”, The 8th International Symposium on Bioinformatics Research and Applications (ISBRA), vol. LNBI 7292. pp. 213-224, 2012.PDF icon ParkNakhleh.pdf (289.57 KB)
H. J. Park and Nakhleh, L., “Inference of Reticulate Evolutionary Histories by Maximum Likelihood: The Performance of Information Criteria”, BMC Bioinformatics, vol. 13, no. S19, p. S12, 2012.PDF icon ParkNakhleh-RECOMBCG12.pdf (754.52 KB)
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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, 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., “ncDNA and drift drive binding site accumulation”, BMC Evolutionary Biology, vol. 12, p. 159, 2012.PDF icon RuthsNakhleh-BMCEvolBiol2012.pdf (659.08 KB)
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, 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 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.
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., “RECOMP: A Parsimony-based Method for Detecting Recombination”, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 59-68.
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., “Recombination and phylogeny: effects and detection”, International Journal on Bioinformatics Research and Applications, vol. 1, pp. 202-212, 2005.

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