Biblio

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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. Zhu and Nakhleh, L., “Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models”, Workshop on Algorithms in Bioinformatics, vol. LNBI 7534. pp. 57-68, 2012.PDF icon ZhuNakhleh-WABI12.pdf (1.53 MB)
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)
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)
Z. Zhu, Liu, X., Ogilvie, H. A., and Nakhleh, L., “A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data”, Bioinformatics (ISMB 19 Proceedings), vol. 35, pp. i370-i378, 2019.PDF icon ZhuEtAl-ISMB19.pdf (668.97 KB)
Y. Zhu, Du, P., and Nakhleh, L., “Gene Duplicability-Connectivity-Complexity Across Organisms and a Neutral Evolutionary Explanation”, PLoS One, vol. 7, no. 9, p. e44491, 2012.PDF icon ZhuDuNakhleh.pdf (217.94 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)
W. Zhou and Nakhleh, L., “Quantifying And Assessing the Effect of Chemical Symmetry in Metabolic Pathways”, Journal of Chemical Information and Modeling, vol. 52, pp. 2684-2696, 2012.PDF icon ZhouNakhleh-JCIM2012.pdf (2.66 MB)
W. Zhou and Nakhleh, L., “Convergent evolution of modularity in metabolic networks through different community structures”, BMC Evolutionary Biology, vol. 12, p. 181, 2012.PDF icon ZhouNakhleh-BMCEvolBiol2012.pdf (1.88 MB)
W. Zhou and Nakhleh, L., “Properties of metabolic graphs: Biological organization or representation artifacts?”, BMC Bioinformatics, vol. 12, p. 132, 2011.PDF icon ZhouNakhleh-BMCBioinfo11.pdf (1.08 MB)
W. Zhou and Nakhleh, L., “The strength of chemical linkage as a criterion for pruning metabolic graphs”, Bioinformatics, vol. 27, no. 14, pp. 1957-1963, 2011.PDF icon ZhouNakhleh-Bioinformatics11.pdf (749.76 KB)
H. Zafar, Tzen, A., Navin, N., Chen, K., and Nakhleh, L., “SiFit: A method for inferring tumor trees from single-cell sequencing data under finite-site models”, Genome Biology, vol. 18, p. 178, 2017.PDF icon ZafarEtAl-GB17.pdf (2.12 MB)
H. Zafar, Navin, N., Chen, K., and Nakhleh, L., “SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data”, Genome Research, 2019.
H. Zafar, Wang, Y., Nakhleh, L., Navin, N., and Chen, K., “Monovar: single nucleotide variant detection in single cells”, Nature Methods, vol. 13, no. 6, pp. 505-507, 2016.PDF icon ZafarEtAl-NMETH2016.pdf (1.51 MB)
H. Zafar, Navin, N., Nakhleh, L., and Chen, K., “Computational approaches for inferring tumor evolution from single-cell genomic data”, Current Opinion in Systems Biology, vol. 7, pp. 16-25, 2017.PDF icon ZafarEtAl-Rev2017.pdf (1.34 MB)
Y
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)
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)
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, Degnan, J. H., and Nakhleh, L., “The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection”, PLoS Genetics, vol. 8, no. 4, p. e1002660, 2012.PDF icon YuDegnanNakhleh.pdf (483.41 KB)
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)

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