Biblio

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BioNetModel
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)
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., “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)
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)
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)
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 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)
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)
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
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance”, in Proceedings of the International Symposium on Bioinformatics Research and Applications, 2007, vol. 4463, pp. 61-72.
L. Nakhleh, Jin, G., Zhao, F., and Mellor-Crummey, J., “Reconstructing phylogenetic networks using maximum parsimony”, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 2005, pp. 93-102.