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.
ZhuEtAl-PLoSCB18.pdf (10.6 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.
ZhuLinNakhleh13.pdf (1.18 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.
ZhuEtAl-ISMB19.pdf (668.97 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.
ZhuYuNakhleh-BMCBioinfo2016.pdf (1.06 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.
ZhuDuNakhleh.pdf (217.94 KB) 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.
ZafarEtAl-Rev2017.pdf (1.34 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.
ZafarEtAl-NMETH2016.pdf (1.51 MB)