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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)
W. Zhou and Nakhleh, L., The strength of chemical linkage as a criterion for pruning metabolic graphs, Bioinformatics, vol. 27, no. 14, pp. 1957-1963, 2011.PDF icon ZhouNakhleh-Bioinformatics11.pdf (749.76 KB)
S. Kamoun, Lozano-Duran, R., and Nakhleh, L., Stranger in a strange land: The experiences of immigrant researchers, Genome Biology, vol. 18, p. 232, 2017.PDF icon Stranger-GB17.pdf (286.06 KB)
T. Warnow, Evans, S. N., Ringe, D., and Nakhleh, L., A Stochastic model of language evolution that incorporates homoplasy and borrowing, Phylogenetic Methods and the Prehistory of Languages, 2004.
C. Than and Nakhleh, L., SPR-based tree reconciliation: Non-binary trees and multiple solutions, in Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC), 2008, pp. 251-260.
C. Than and Nakhleh, L., Species tree inference by minimizing deep coalescences, PLoS Computational Biology, vol. 5, p. e1000501, 2009.
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)
D. Ruths, Muller, M., Tseng, J. T., Nakhleh, L., and Ram, P. T., The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizing the Dynamics of Cell-specific Signaling Networks, PLoS Computational Biology, vol. 4, p. e1000005, 2008.
H. Zafar, Tzen, A., Navin, N., Chen, K., and Nakhleh, L., SiFit: A method for inferring tumor trees from single-cell sequencing data under finite-site models, Genome Biology, vol. 18, p. 178, 2017.PDF icon ZafarEtAl-GB17.pdf (2.12 MB)
H. Zafar, Navin, N., Chen, K., and Nakhleh, L., SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data, Genome Research, 2019.
I. A. Kanj, Nakhleh, L., Than, C., and Xia, G., Seeing the trees and their branches in the network is hard, Theoretical Computer Science, vol. 401, pp. 153-164, 2008.
I. A. Kanj, Nakhleh, L., Than, C., and Xia, G., Seeing the trees and their branches in the network is hard, in Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS), 2007, pp. 82-93.
L. Nakhleh, Ruths, D., and Wang, L. S., RIATA-HGT: A Fast and accurate heuristic for reconstrucing horizontal gene transfer, in Proceedings of the Eleventh International Computing and Combinatorics Conference (COCOON 05), 2005, vol. 3595, pp. 84-93.
L. Nakhleh, Review of ReCombinatorics by Dan Gusfield, SIAM Review, vol. 57, no. 4, pp. 638-642, 2015.PDF icon SIAMReviews-Recombinatorics.pdf (177.2 KB)
D. Wen, Yu, Y., Hahn, M. W., and Nakhleh, L., Reticulate Evolutionary History and Extensive Introgression in Mosquito Species Revealed by Phylogenetic Network Analysis, Molecular Ecology, vol. 25, pp. 2361-2372, 2016.PDF icon WenEtAl-MolEcol2016.pdf (1.26 MB)
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.
E. Erdem, Lifschitz, V., Nakhleh, L., and Ringe, D., Reconstructing the Evolutionary History of Indo-European Languages using Answer Set Programming, in Proceedings of the Fifth International Symposium on Practical Aspects of Declarative Languages (PADL 2003), 2003, vol. 2562, pp. 160-176.
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)
L. Nakhleh, Warnow, T., Linder, C. R., and John, S. K., Reconstructing reticulate evolution in species–theory and practice, in Journal of Computational Biology, 2005, vol. 12(6-7), pp. 796-811.
L. Nakhleh, Warnow, T., and Linder, C. R., Reconstructing reticulate evolution in species–theory and practice, in Proc.\ 8th Ann.İnt’l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB04}), 2004, pp. 337–346.
L. Nakhleh, Jin, G., Zhao, F., and Mellor-Crummey, J., Reconstructing phylogenetic networks using maximum parsimony, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 2005, pp. 93-102.