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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 and Nakhleh, L., Species tree inference by minimizing deep coalescences, PLoS Computational Biology, vol. 5, p. e1000501, 2009.
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.
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.
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.
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.
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.
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.
Y. Wang and Nakhleh, L., Towards an Accurate and Efficient Heuristic for Species/Gene Tree Co-estimation, Bioinformatics, vol. 34, pp. i697-i705, 2018.PDF icon WangNakhleh-ECCB18.pdf (1.8 MB)
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)
T. Warnow, Evans, S. N., Ringe, D., and Nakhleh, L., A Stochastic model of language evolution that incorporates homoplasy and borrowing, Phylogenetic Methods and the Prehistory of Languages, 2004.
D. Wen and Nakhleh, L., Co-estimating reticulate phylogenies and gene trees from multi-locus sequence data, Systematic Biology, vol. 67, no. 3, pp. 439-457, 2018.PDF icon WenNakhleh-SysBio2018PlusSI.pdf (5.92 MB)
D. Wen, Yu, Y., Zhu, J., and Nakhleh, L., Inferring phylogenetic networks using PhyloNet, Systematic Biology, vol. 67, no. 4, pp. 735-740, 2018.PDF icon phylonet3.pdf (144.21 KB)
D. Wen, Yu, Y., and Nakhleh, L., Bayesian inference of species phylogenies under the multispecies network coalescent, PLoS Genetics, vol. 12, no. 5, p. e1006006, 2016.PDF icon WenEtAl-PLoSGenetics2016.pdf (2.11 MB)
D. Wen, Yu, Y., Hahn, M. W., and Nakhleh, L., Reticulate Evolutionary History and Extensive Introgression in Mosquito Species Revealed by Phylogenetic Network Analysis, Molecular Ecology, vol. 25, pp. 2361-2372, 2016.PDF icon WenEtAl-MolEcol2016.pdf (1.26 MB)
Y. Yu, Ristic, N., and Nakhleh, L., Fast Algorithms and Heuristics for Phylogenomics under ILS and Hybridization, BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.PDF icon YuRisticNakhleh13.pdf (1.68 MB)
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)
Y. Yu, Barnett, R. M., and Nakhleh, L., Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting, Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.PDF icon YuEtAl-SystBiol2013.pdf (1.55 MB)
Y. Yu, Dong, J., Liu, K., and Nakhleh, L., Maximum Likelihood Inference of Reticulate Evolutionary Histories, Proceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.PDF icon PNAS-2014-YuEtAl.pdf (1.55 MB)
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)
Y. Yu and Nakhleh, L., A Maximum Pseudo-likelihood Approach for Phylogenetic Networks, BMC Genomics, vol. 16, no. Suppl 10, p. S10, 2015.PDF icon YuNakhleh-BMCGenomics2015.pdf (1.75 MB)
Y. Yu, Warnow, T., and Nakhleh, L., Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles, Journal of Computational Biology, vol. 18, no. 11, pp. 1543-1559, 2011.PDF icon YuWarnowNakhleh-JCB11.pdf (419.4 KB)