Biblio

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Conference Paper
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.
C. Coarfa, Dotsenko, Y., Mellor-Crummey, J., Nakhleh, L., and Roshan, U., PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction, in Proceedigns of the First IEEE Workshop on High Performance Computing in Medicine and Biology, 2005, vol. 2, pp. 346-350.
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.
P. Du, Ogilvie, H. A., and Nakhleh, L., Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks, in The International Symposium on Bioinformatics Research and Applications (ISBRA), 2019.PDF icon DuEtAl-ISBRA19.pdf (417.76 KB)
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)
P. Du and Nakhleh, L., Species tree and reconciliation estimation under a duplication-loss-coalescence model, The 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). pp. 376-385, 2018.PDF icon DuNakhleh18.pdf (1.28 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)
Y. Yu, Than, C., Degnan, J. H., and Nakhleh, L., Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting, Systematic Biology, vol. 60, pp. 138-149, 2011.PDF icon YuEtAl-SB11.pdf (696.39 KB)
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)
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)
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)
Y. Yu, Dong, J., Liu, K., and Nakhleh, L., Maximum Likelihood Inference of Reticulate Evolutionary Histories, Proceedings of the National Academy of Sciences, vol. 111, no. 46, pp. 16448-16453, 2014.PDF icon PNAS-2014-YuEtAl.pdf (1.55 MB)
Y. Dotsenko, Coarfa, C., Nakhleh, L., Mellor-Crummey, J., and Roshan, U., PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction, International Journal on Bioinformatics Research and Applications, vol. 2, pp. 407-419, 2006.
Y. Yu, Degnan, J. H., and Nakhleh, L., The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection, PLoS Genetics, vol. 8, no. 4, p. e1002660, 2012.PDF icon YuDegnanNakhleh.pdf (483.41 KB)