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PhyloNet
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.
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.
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)
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, 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.
Y. Yu, Than, C., Degnan, J. H., and Nakhleh, L., Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting, Systematic Biology, vol. 60, pp. 138-149, 2011.PDF icon YuEtAl-SB11.pdf (696.39 KB)
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, 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 and Wang, L. S., Phylogenetic networks, trees, and clusters, in Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA 05), 2005, vol. 3515, pp. 919-926.
L. Nakhleh, Evolutionary phylogenetic networks: models and issues, in The Problem Solving Handbook for Computational Biology and Bioinformatics, L. Heath and Ramakrishnan, N., Eds. Springer, 2010, pp. 125-158.PDF icon HeathRamakrishnanBookChapter.pdf (381.74 KB)
B. M. E. Moret, Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J., and Timme, R., Phylogenetic networks: modeling, reconstructibility, and accuracy, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, pp. 13–23, 2004.
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.

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