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C. Than, Sugino, R., Innan, H., and Nakhleh, L., Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data, Bioinformatics, vol. 24, pp. i123-i131, 2008.
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. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 MB)
Z. Cao, Zhu, J., and Nakhleh, L., Empirical performance of tree-based inference of phylogenetic networks, in Workshop on Algorithms in Bioinformatics (WABI), 2019.PDF icon CaoEtAl-WABI19.pdf (1.2 MB)
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.
N. Berestovsky and Nakhleh, L., An Evaluation of Methods for Inferring Boolean Networks from Time-series Data, PLoS One, vol. 8, p. e66031, 2013.PDF icon BerestovskyNakhleh-PLoSOne13.pdf (942.99 KB)
Y. Zhu, Lin, Z., and Nakhleh, L., Evolution After Whole-genome Duplication: A Network Perspective, G3: Genes | Genomes | Genetics, vol. 3, no. 11, pp. 2049-2057, 2013.PDF icon ZhuLinNakhleh13.pdf (1.18 MB)
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)
F. Barbancon, Evans, S., Nakhleh, L., Ringe, D., and Warnow, T., An experimental study comparing linguistic phylogenetic reconstruction methods, Diachronica, vol. 30, no. 2, pp. 143-170, 2013.PDF icon Diachronica13.pdf (575.02 KB)
Y. Yu, Jermaine, C., and Nakhleh, L., Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks, BMC Genomics, vol. 17, no. Suppl 10, p. 784, 2016.PDF icon YuJermaineNakhleh-BMCGenomics2016.pdf (965.19 KB)
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.
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.
J. Zhu, Yu, Y., and Nakhleh, L., In the light of deep coalescence: Revisiting trees within networks, BMC Bioinformatics, vol. 17, no. Suppl 14, p. 415, 2016.PDF icon ZhuYuNakhleh-BMCBioinfo2016.pdf (1.06 MB)
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.
H. J. Park and Nakhleh, L., Inference of Reticulate Evolutionary Histories by Maximum Likelihood: The Performance of Information Criteria, BMC Bioinformatics, vol. 13, no. S19, p. S12, 2012.PDF icon ParkNakhleh-RECOMBCG12.pdf (754.52 KB)
J. Zhu and Nakhleh, L., Inference of species phylogenies from bi-allelic markers using pseudo-likelihood, Bioinformatics, vol. 34, pp. i376-385, 2018.PDF icon ZhuNakhleh-ISMB18.pdf (1.26 MB)
R. A. L. Elworth and Nakhleh, L., Inferring local genealogies on closely related genomes, RECOMB Comparative Genomics, vol. LNBI 10562. pp. 213-231, 2017.PDF icon ElworthNakhleh-RECOMBCG17.pdf (2.81 MB)