Biblio

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Journal Article
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 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)
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)
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)
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, 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)
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)
J. Zhu, Wen, D., Yu, Y., Meudt, H., and Nakhleh, L., “Bayesian inference of phylogenetic networks from bi-allelic genetic markers”, PLoS Computational Biology, vol. 14, no. 1, p. e1005932, 2018.PDF icon ZhuEtAl-PLoSCB18.pdf (10.6 MB)
Conference Proceedings
Y. Yu and Nakhleh, L., “A Distance-based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting”, International Symposium on Bioinformatics Research and Applications (ISBRA), vol. Lecture Notes in Bioinformatics 9096. pp. 378-389, 2015.PDF icon YuNakhleh-ISBRA15.pdf (327.21 KB)
Y. Yu, Warnow, T., and Nakhleh, L., “Algorithms for MDC-based multi-locus phylogeny inference”, The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), vol. LNBI 6577. Lecture Notes in Bioinformatics, pp. 531-545, 2011.PDF icon YuWarnowNakhleh-RECOMB11.pdf (369.65 KB)