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Journal Article
G. Saxer, Krepps, M. D., Merkley, E. D., Ansong, C., Kaiser, B. L. Deatherage, Valovska, M. - T., Ristic, N., Yeh, P. T., Prakash, V. P., Leiser, O. P., Nakhleh, L., Gibbons, H. S., Kreuzer, H. W., and Shamoo, Y., Mutations in global regulators lead to metabolic selection during adaptation to complex environments, PLoS Genetics, vol. 10, no. 12, p. e1004872, 2014.PDF icon SaxerEtAl-PLoSGenetics2014.pdf (1.99 MB)
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.
L. Nakhleh, Ringe, D., and Warnow, T., Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages, LANGUAGE, Journal of the Linguistic Society of America, vol. 81, pp. 382-420, 2005.
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 and Wang, L. S., Phylogenetic Networks: Properties and Relationship to Trees and Clusters, LNCS Transactions on Computational Systems Biology, II, vol. 3680, pp. 82-99, 2005.
C. Than, Ruths, D., and Nakhleh, L., PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships, BMC Bioinformatics, vol. 9, p. 322, 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)
Y. Wang, Ogilvie, H. A., and Nakhleh, L., Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees, Molecular Biology and Evolution, vol. 37, pp. 1809-1818, 2020.PDF icon MBE2020.pdf (502.98 KB)
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.
W. Zhou and Nakhleh, L., Properties of metabolic graphs: Biological organization or representation artifacts?, BMC Bioinformatics, vol. 12, p. 132, 2011.PDF icon ZhouNakhleh-BMCBioinfo11.pdf (1.08 MB)
D. Ruths, Nakhleh, L., and Ram, P. T., Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle, BMC Systems Biology, vol. 2, p. 76, 2008.
D. Ruths and Nakhleh, L., Recombination and phylogeny: effects and detection, International Journal on Bioinformatics Research and Applications, vol. 1, pp. 202-212, 2005.
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, Review of ReCombinatorics by Dan Gusfield, SIAM Review, vol. 57, no. 4, pp. 638-642, 2015.PDF icon SIAMReviews-Recombinatorics.pdf (177.2 KB)
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.
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.
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)
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.
C. Than and Nakhleh, L., Species tree inference by minimizing deep coalescences, PLoS Computational Biology, vol. 5, p. e1000501, 2009.
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.
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)
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)
Y. Wang and Nakhleh, L., Towards an Accurate and Efficient Heuristic for Species/Gene Tree Co-estimation, Bioinformatics, vol. 34, pp. i697-i705, 2018.PDF icon WangNakhleh-ECCB18.pdf (1.8 MB)