Biblio

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Conference Paper
C. Than, Ruths, D., Innan, H., and Nakhleh, L., Identifiability issues in phylogeny-based detection of horizontal gene transfer, in Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop, 2006, vol. 4205, pp. 215-219.
L. Nakhleh, Miranker, D., Barbancon, F., Piel, W. H., and Donoghue, M. J., Requirements of Phylogenetic Databases, in Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003), 2003, pp. 141-148.
Conference Proceedings
R. A. L. Elworth, Allen, C., Benedict, T., Dulworth, P., and Nakhleh, L., DGEN: A Test Statistic for Detection of General Introgression Scenarios, Workshop on Algorithms in Bioinformatics (WABI), vol. LIPIcs 19. pp. 19:1 - 19:13, 2018.PDF icon dgen.pdf (547.19 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)
Journal Article
R. A. L. Elworth, Allen, C., Benedict, T., Dulworth, P., and Nakhleh, L., ALPHA: A toolkit for automated local phylogenomic analyses, Bioinformatics, vol. 34, no. 16, pp. 2848-2850, 2018.PDF icon Alpha.pdf (211.74 KB)
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)
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)
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)
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 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)
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)
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)
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)
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)