Biblio

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W. Zhou and Nakhleh, L., Properties of metabolic graphs: Biological organization or representation artifacts?, BMC Bioinformatics, vol. 12, p. 132, 2011.PDF icon ZhouNakhleh-BMCBioinfo11.pdf (1.08 MB)
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. 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. Wang, Ogilvie, H. A., and Nakhleh, L., Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees, Molecular Biology and Evolution, vol. 37, pp. 1809-1818, 2020.PDF icon MBE2020.pdf (502.98 KB)
Z. Cao, Liu, X., Ogilvie, H. A., Yan, Z., and Nakhleh, L., Practical Aspects of Phylogenetic Network Analysis Using PhyloNet, 2019.
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)
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 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 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.
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.
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.
N. Berestovsky, Fukui, R., and Nakhleh, L., On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks., Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. pp. 184-191, 2012.PDF icon BerestovskyFukuiNakhleh.pdf (2.77 MB)
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.
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.
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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