Biblio

2014
K. Liu, Dai, J., Truong, K., Song, Y., Kohn, M. H., and Nakhleh, L., An HMM-based comparative genomic framework for detecting introgression in eukaryotes, PLoS Computational Biology, vol. 10, no. 6, p. e1003649, 2014.PDF icon LiuEtAl-PLoSCB14.pdf (1.3 MB)
S. Iadevaia, Nakhleh, L., Azencott, R., and Ram, P. T., Mapping network motif tunability and robustness in the design of synthetic signaling circuits, PLoS One, vol. 9, no. 3, p. e91743, 2014.PDF icon IadevaiaEtAl-PLoSOne14.pdf (1.01 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)
G. Saxer, Krepps, M. D., Merkley, E. D., Ansong, C., Kaiser, B. L. Deatherage, Valovska, M. - T., Ristic, N., Yeh, P. T., Prakash, V. P., Leiser, O. P., Nakhleh, L., Gibbons, H. S., Kreuzer, H. W., and Shamoo, Y., Mutations in global regulators lead to metabolic selection during adaptation to complex environments, PLoS Genetics, vol. 10, no. 12, p. e1004872, 2014.PDF icon SaxerEtAl-PLoSGenetics2014.pdf (1.99 MB)
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)
2016
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)
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)
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)
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)
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)

Pages