Biblio

2016
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)
2015
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)
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)
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)
L. Nakhleh, “Review of ReCombinatorics by Dan Gusfield”, SIAM Review, vol. 57, no. 4, pp. 638-642, 2015.PDF icon SIAMReviews-Recombinatorics.pdf (177.2 KB)
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)
2013
T. Ruths and Nakhleh, L., “Boosting forward-time population genetic simulators through genotype compression”, BMC Bioinformatics, vol. 14, p. 192, 2013.PDF icon RuthsNakhleh-BMCBioinfo13.pdf (680.55 KB)
L. Nakhleh, “Computational approaches to species phylogeny inference and gene tree reconciliation”, Trends in Ecology and Evolution, vol. 28, no. 12, pp. 719-728, 2013.PDF icon TREE-Nakhleh13.pdf (559.43 KB)
N. Berestovsky and Nakhleh, L., “An Evaluation of Methods for Inferring Boolean Networks from Time-series Data”, PLoS One, vol. 8, p. e66031, 2013.PDF icon BerestovskyNakhleh-PLoSOne13.pdf (942.99 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)
F. Barbancon, Evans, S., Nakhleh, L., Ringe, D., and Warnow, T., “An experimental study comparing linguistic phylogenetic reconstruction methods”, Diachronica, vol. 30, no. 2, pp. 143-170, 2013.PDF icon Diachronica13.pdf (575.02 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)
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)
E. Bapteste, van Iersel, L., Janke, A., Kelchner, S., Kelk, S., McInerney, J. O., Morrison, D. A., Nakhleh, L., Steel, M., Stougie, L., and Whitfield, J., “Networks: Expanding evolutionary thinking”, Trends in Genetics, vol. 29, no. 8, pp. 439-441, 2013.PDF icon TIG2013.pdf (179.16 KB)
T. Ruths and Nakhleh, L., “Neutral forces acting on intragenomic variability shape the E. coli regulatory network topology”, Proceedings of the National Academy of Sciences, vol. 110, no. 19, pp. 7754-7759, 2013.PDF icon RuthsNakhleh-PNAS13.pdf (2.57 MB)
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)
2012
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)

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