Biblio

Export 38 results:
Author Keyword Title Type [ Year(Asc)]
Filters: Keyword is PhyloNet  [Clear All Filters]
2014
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. 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)
2013
L. Nakhleh, “Computational approaches to species phylogeny inference and gene tree reconciliation”, Trends in Ecology and Evolution, vol. 28, no. 12, pp. 719-728, 2013.PDF icon TREE-Nakhleh13.pdf (559.43 KB)
Y. Yu, Ristic, N., and Nakhleh, L., “Fast Algorithms and Heuristics for Phylogenomics under ILS and Hybridization”, BMC Bioinformatics, vol. 14, no. Suppl 15, p. S6, 2013.PDF icon YuRisticNakhleh13.pdf (1.68 MB)
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)
Y. Yu, Barnett, R. M., and Nakhleh, L., “Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting”, Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.PDF icon YuEtAl-SystBiol2013.pdf (1.55 MB)
2012
H. J. Park and Nakhleh, L., “Inference of Reticulate Evolutionary Histories by Maximum Likelihood: The Performance of Information Criteria”, BMC Bioinformatics, vol. 13, no. S19, p. S12, 2012.PDF icon ParkNakhleh-RECOMBCG12.pdf (754.52 KB)
H. J. Park and Nakhleh, L., “MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees”, The 8th International Symposium on Bioinformatics Research and Applications (ISBRA), vol. LNBI 7292. pp. 213-224, 2012.PDF icon ParkNakhleh.pdf (289.57 KB)
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. 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)
2011
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)
2010
H. J. Park, Jin, G., and Nakhleh, L., “Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees”, Proceedings of the 9th Annual International Conference on Computational Systems Biology. pp. 114-123, 2010.PDF icon ParkEtAl-CSB2010.pdf (946.56 KB)
H. J. Park, Jin, G., and Nakhleh, L., “Bootstrap-based support of HGT inferred by maximum parsimony”, BMC Evolutionary Biology, vol. 10, p. 131, 2010.PDF icon BMCEvolBiol2010.pdf (1.18 MB)
L. Nakhleh, “Evolutionary phylogenetic networks: models and issues”, in The Problem Solving Handbook for Computational Biology and Bioinformatics, L. Heath and Ramakrishnan, N., Eds. Springer, 2010, pp. 125-158.PDF icon HeathRamakrishnanBookChapter.pdf (381.74 KB)
L. Nakhleh, “A metric on the space of reduced phylogenetic networks”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, pp. 218-222, 2010.PDF icon tcbb-Metric.pdf (287.01 KB)
2009
L. Nakhleh, Ruths, D., and Innan, H., “Gene trees, species trees, and species networks”, in Meta-analysis and Combining Information in Genetics, R. Guerra and Goldstein, D., Eds. Chapman & Hall, CRC Press, 2009, pp. 275-293.
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.
2008
I. A. Kanj, Nakhleh, L., and Xia, G., “The compatibility of binary characters on phylogenetic networks: Complexity and parameterized algorithms”, Algorithmica, vol. 51, pp. 99-128, 2008.
G. Jin, Nakhleh, L., and Than, C., “Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer”, in Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop, 2008, vol. 5267, pp. 113-127.
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.
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.
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.
2007
C. Than, Ruths, D., Innan, H., and Nakhleh, L., “Confounding Factors in {HGT} Detection: Statistical Error, Coalescent Effects, and Multiple Solutions”, Journal of Computational Biology, vol. 14, pp. 517-535, 2007.
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.

Pages