Biblio

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BioNetModel
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)
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)
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)
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)
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)
CancerGenomics
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)
Epidemiology
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)
NetEvol
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)
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)
T. Ruths and Nakhleh, L., “ncDNA and drift drive binding site accumulation”, BMC Evolutionary Biology, vol. 12, p. 159, 2012.PDF icon RuthsNakhleh-BMCEvolBiol2012.pdf (659.08 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)
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)
Network evolution
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)
PhyloNet
H. J. Park and Nakhleh, L., “MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees”, The 8th International Symposium on Bioinformatics Research and Applications (ISBRA), vol. LNBI 7292. pp. 213-224, 2012.PDF icon ParkNakhleh.pdf (289.57 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)
H. J. Park and Nakhleh, L., “Inference of Reticulate Evolutionary Histories by Maximum Likelihood: The Performance of Information Criteria”, BMC Bioinformatics, vol. 13, no. S19, p. S12, 2012.PDF icon ParkNakhleh-RECOMBCG12.pdf (754.52 KB)
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)
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, 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, 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)
Trees
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)
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, 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)