Biblio

Export 98 results:
Author Keyword Title Type [ Year(Asc)]
2013
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)
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)
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)
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)
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)
N. Berestovsky, Fukui, R., and Nakhleh, L., “On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks.”, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. pp. 184-191, 2012.PDF icon BerestovskyFukuiNakhleh.pdf (2.77 MB)
S. Takuno, Kado, T., Sugino, R. P., Nakhleh, L., and Innan, H., “Population genomics in bacteria: A case study of Staphylococcus aureus.”, Molecular Biology and Evolution, vol. 29, no. 2, pp. 797-800, 2012.PDF icon TakunoEtAl-MBE11.pdf (933.28 KB)
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)
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)
Y. Zhu and Nakhleh, L., “Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models”, Workshop on Algorithms in Bioinformatics, vol. LNBI 7534. pp. 57-68, 2012.PDF icon ZhuNakhleh-WABI12.pdf (1.53 MB)
2011
Y. Yu, Warnow, T., and Nakhleh, L., “Algorithms for MDC-based multi-locus phylogeny inference”, The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), vol. LNBI 6577. Lecture Notes in Bioinformatics, pp. 531-545, 2011.PDF icon YuWarnowNakhleh-RECOMB11.pdf (369.65 KB)
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)
Y. Yu, Than, C., Degnan, J. H., and Nakhleh, L., “Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting”, Systematic Biology, vol. 60, pp. 138-149, 2011.PDF icon YuEtAl-SB11.pdf (696.39 KB)
Y. Lu, Muller, M., Smith, D., Dutta, B., Mourov, K., Iadevaia, S., Ruths, D., Tseng, J. - T., Yu, S., Yu, Q., Nakhleh, L., Balazsi, G., Donnelly, J., Schurdak, M., Morgan-Lappe, S., Fesik, S., Ram, P. T., and Mills, G. B., “Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling”, Oncogene, vol. 30, pp. 4567-4577, 2011.PDF icon Oncogene2011.pdf (905.3 KB)
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., “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)
2010
H. J. Park, Jin, G., and Nakhleh, L., “Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees”, Proceedings of the 9th Annual International Conference on Computational Systems Biology. pp. 114-123, 2010.PDF icon ParkEtAl-CSB2010.pdf (946.56 KB)
H. J. Park, Jin, G., and Nakhleh, L., “Bootstrap-based support of HGT inferred by maximum parsimony”, BMC Evolutionary Biology, vol. 10, p. 131, 2010.PDF icon BMCEvolBiol2010.pdf (1.18 MB)
D. Ruths and Nakhleh, L., “Deriving predictive models of signaling network dynamics from qualitative experimental data”, in Proceedings of the 9th Annual International Conference on Computational Systems Biology, 2010.PDF icon RuthsNakhleh-CSB2010.pdf (548.82 KB)
L. Nakhleh, “Evolutionary phylogenetic networks: models and issues”, in The Problem Solving Handbook for Computational Biology and Bioinformatics, L. Heath and Ramakrishnan, N. Springer, 2010, pp. 125-158.PDF icon HeathRamakrishnanBookChapter.pdf (381.74 KB)
C. Than and Nakhleh, L., “Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences”, in Estimating Species Trees: Practical and Theoretical Aspects, L. L. Knowles and Kubatko, L. S. Wiley-VCH, 2010.

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