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PhyloNet
I. A. Kanj, Nakhleh, L., and Xia, G., The compatibility of binary characters on phylogenetic networks: Complexity and parameterized algorithms, Algorithmica, vol. 51, pp. 99-128, 2008.
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., Efficient parsimony-based methods for phylogenetic network reconstruction, Bioinformatics, vol. 23, pp. e123-e128, 2006.
L. Nakhleh and Wang, L. S., Phylogenetic Networks: Properties and Relationship to Trees and Clusters, LNCS Transactions on Computational Systems Biology, II, vol. 3680, pp. 82-99, 2005.
I. A. Kanj, Nakhleh, L., Than, C., and Xia, G., Seeing the trees and their branches in the network is hard, Theoretical Computer Science, vol. 401, pp. 153-164, 2008.
I. A. Kanj, Nakhleh, L., Than, C., and Xia, G., Seeing the trees and their branches in the network is hard, in Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS), 2007, pp. 82-93.
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.
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)
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.
C. Than and Nakhleh, L., SPR-based tree reconciliation: Non-binary trees and multiple solutions, in Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC), 2008, pp. 251-260.
S. Takuno, Kado, T., Sugino, R. P., Nakhleh, L., and Innan, H., Population genomics in bacteria: A case study of Staphylococcus aureus., Molecular Biology and Evolution, vol. 29, no. 2, pp. 797-800, 2012.PDF icon TakunoEtAl-MBE11.pdf (933.28 KB)
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.
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.
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.
C. Than, Ruths, D., Innan, H., and Nakhleh, L., Confounding Factors in {HGT} Detection: Statistical Error, Coalescent Effects, and Multiple Solutions, Journal of Computational Biology, vol. 14, pp. 517-535, 2007.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., Maximum likelihood of phylogenetic networks, Bioinformatics, vol. 22, pp. 2604-2611, 2006.
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)
C. R. Linder, Moret, B. M. E., Nakhleh, L., and Warnow, T., Network (reticulate) evolution: biology, models, and algorithms, in The Ninth Pacific Symposium on Biocomputing (PSB), 2004.
Trees
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.
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, 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.
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 and Nakhleh, L., Recombination and phylogeny: effects and detection, International Journal on Bioinformatics Research and Applications, vol. 1, pp. 202-212, 2005.
C. Than and Nakhleh, L., Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences, in Estimating Species Trees: Practical and Theoretical Aspects, L. L. Knowles and Kubatko, L. S., Eds. Wiley-VCH, 2010.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., Designing Fast Converging Phylogenetic Methods, Bioinformatics, vol. 17, pp. S190–S198, 2001.

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