Biblio

Journal Article
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)
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)
W. Zhou and Nakhleh, L., “Quantifying And Assessing the Effect of Chemical Symmetry in Metabolic Pathways”, Journal of Chemical Information and Modeling, vol. 52, pp. 2684-2696, 2012.PDF icon ZhouNakhleh-JCIM2012.pdf (2.66 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)
X. Fan, Zhou, W., Chong, Z., Nakhleh, L., and Chen, K., “Towards accurate characterization of clonal heterogeneity based on structural variation”, BMC Bioinformatics, vol. 15, p. 299, 2014.PDF icon FanEtAl2014.pdf (2.04 MB)
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)

Pages