Biblio

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2018
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)
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)
2017
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)
2016
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)
M. W. Hahn and Nakhleh, L., “Irrational Exuberance for Resolved Species Trees”, Evolution, vol. 70, no. 1, pp. 7-17, 2016.PDF icon HahnNakhleh2016.pdf (433.49 KB)
2015
K. Liu, Steinberg, E., Yozzo, A., Song, Y., Kohn, M. H., and Nakhleh, L., “Interspecific introgressive origin of genomic diversity in the house mouse”, Proceedings of the National Academy of Sciences, vol. 112, no. 1, pp. 196-201, 2015.PDF icon LiuEtAl-PNAS2014.pdf (24.54 MB)
2012
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)
2010
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.
2008
G. Jin, Nakhleh, L., and Than, C., “Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer”, in Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop, 2008, vol. 5267, pp. 113-127.
2007
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.
2006
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.