Biblio

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Book Chapter
R. A. L. Elworth, Ogilvie, H. A., Zhu, J., and Nakhleh, L., Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization, in Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, vol. 29, Cham: Springer, 2019.PDF icon ElworthZhuOgilvieNakhleh.pdf (743.9 KB)
Journal Article
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)
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)
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)
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, 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)
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, 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)
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)
B. J. Grindel, Martinez, J. R., Tellman, T. V., Harrington, D. A., Zafar, H., Nakhleh, L., Chung, L., and Farach-Carson, M. C., Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells, Scientific Reports, vol. 8, p. 7262, 2018.PDF icon GrindelEtAl.pdf (2.28 MB)
N. Berestovsky, Zhou, W., Nagrath, D., and Nakhleh, L., Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks, PLoS Computational Biology, vol. 9, no. 11, p. e1003306, 2013.PDF icon BerestovskyEtAl13.pdf (1.66 MB)
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)
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., 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)
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, 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)
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)
X. Fan, Zhou, W., Chong, Z., Nakhleh, L., and Chen, K., Towards accurate characterization of clonal heterogeneity based on structural variation, BMC Bioinformatics, vol. 15, p. 299, 2014.PDF icon FanEtAl2014.pdf (2.04 MB)