Biblio

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PhyloNet
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.
K. Liu, Dai, J., Truong, K., Song, Y., Kohn, M. H., and Nakhleh, L., “An HMM-based comparative genomic framework for detecting introgression in eukaryotes”, PLoS Computational Biology, vol. 10, no. 6, p. e1003649, 2014.PDF icon LiuEtAl-PLoSCB14.pdf (1.3 MB)
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.
Trees
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.
T. Shigaki, Rees, I., Nakhleh, L., and Hirschi, K., “Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters”, Journal of Molecular Evolution, vol. 63, pp. 815-825, 2006.
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.
C. Than and Nakhleh, L., “Species tree inference by minimizing deep coalescences”, PLoS Computational Biology, vol. 5, p. e1000501, 2009.
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.
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.

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