Biblio

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BioNetModel
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)
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)
Epidemiology
C. Than, Sugino, R., Innan, H., and Nakhleh, L., “Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data”, Bioinformatics, vol. 24, pp. i123-i131, 2008.
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)
PhyloNet
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 495-505, 2009.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Inferring phylogenetic networks by the maximum parsimony criterion: a case study”, Molecular Biology and Evolution, vol. 24, pp. 324-337, 2007.
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.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Efficient parsimony-based methods for phylogenetic network reconstruction”, Bioinformatics, vol. 23, pp. e123-e128, 2006.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Maximum likelihood of phylogenetic networks”, Bioinformatics, vol. 22, pp. 2604-2611, 2006.
B. M. E. Moret, Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J., and Timme, R., “Phylogenetic networks: modeling, reconstructibility, and accuracy”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, pp. 13–23, 2004.
L. Nakhleh, Sun, J., Warnow, T., Linder, R., Moret, B. M. E., and Tholse, A., “Towards the development of tools for evaluating phylogenetic network reconstruction methods”, in Proc.\ 8th Pacific Symp. on Biocomputing ({PSB03}), 2003, pp. 315–326.
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)
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)
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)
K. Liu, Dai, J., Truong, K., Song, Y., Kohn, M. H., and Nakhleh, L., “An HMM-based comparative genomic framework for detecting introgression in eukaryotes”, PLoS Computational Biology, vol. 10, no. 6, p. e1003649, 2014.PDF icon LiuEtAl-PLoSCB14.pdf (1.3 MB)
Trees
C. Than, Sugino, R., Innan, H., and Nakhleh, L., “Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data”, Bioinformatics, vol. 24, pp. i123-i131, 2008.
T. Shigaki, Rees, I., Nakhleh, L., and Hirschi, K., “Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters”, Journal of Molecular Evolution, vol. 63, pp. 815-825, 2006.
Z. Du, Stamatakis, A., Lin, F., Roshan, U., and Nakhleh, L., “Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood”, in Proceedings of the 2005 International Conference on High Performance Computing and Communications, 2005, vol. 2, pp. 346-350.
L. Nakhleh, Moret, B. M. E., Roshan, U., John, S. K., Sun, J., and Warnow, T., “The Accuracy of Phylogenetic Methods for Large Datasets”, in Proc.\ 7th Pacific Symp. on Biocomputing ({PSB02}), 2002, vol. 7, pp. 211-222.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., “Designing Fast Converging Phylogenetic Methods”, Bioinformatics, vol. 17, pp. S190–S198, 2001.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., “The Performance of Phylogenetic Methods on Trees of Bounded Diameter”, in First International Workshop on Algorithms in Bioinformatics (WABI 01), 2001, vol. Lecture Notes in Computer Science 2149, pp. 214–226.