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G. Jin, Nakhleh, L., Snir, S., and Tuller, T., Inferring phylogenetic networks by the maximum parsimony criterion: a case study, Molecular Biology and Evolution, vol. 24, pp. 324-337, 2007.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., Maximum likelihood of phylogenetic networks, Bioinformatics, vol. 22, pp. 2604-2611, 2006.
G. Jin, Nakhleh, L., and Than, C., Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer, in Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop, 2008, vol. 5267, pp. 113-127.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance, in Proceedings of the International Symposium on Bioinformatics Research and Applications, 2007, vol. 4463, pp. 61-72.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., Efficient parsimony-based methods for phylogenetic network reconstruction, Bioinformatics, vol. 23, pp. e123-e128, 2006.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 495-505, 2009.
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, 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, 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, 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.
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.
L. Nakhleh, Jin, G., Zhao, F., and Mellor-Crummey, J., Reconstructing phylogenetic networks using maximum parsimony, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 2005, pp. 93-102.
L. Nakhleh, Review of ReCombinatorics by Dan Gusfield, SIAM Review, vol. 57, no. 4, pp. 638-642, 2015.PDF icon SIAMReviews-Recombinatorics.pdf (177.2 KB)
L. Nakhleh, Moret, B. M. E., Roshan, U., John, S. K., Sun, J., and Warnow, T., The Accuracy of Phylogenetic Methods for Large Datasets, in Proc.\ 7th Pacific Symp. on Biocomputing ({PSB02}), 2002, vol. 7, pp. 211-222.
L. Nakhleh, Warnow, T., Ringe, D., and Evans, S. N., A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset, Transactions of the Philological Society, vol. 3, pp. 171-192, 2005.