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G. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 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)
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, 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)
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)
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)