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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)
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)
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)
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)