Biblio

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Journal Article
L. Nakhleh, Warnow, T., Ringe, D., and Evans, S. N., A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset, Transactions of the Philological Society, vol. 3, pp. 171-192, 2005.
D. Wen and Nakhleh, L., Co-estimating reticulate phylogenies and gene trees from multi-locus sequence data, Systematic Biology, vol. 67, no. 3, pp. 439-457, 2018.PDF icon WenNakhleh-SysBio2018PlusSI.pdf (5.92 MB)
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)
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)
D. Wen, Yu, Y., and Nakhleh, L., Bayesian inference of species phylogenies under the multispecies network coalescent, PLoS Genetics, vol. 12, no. 5, p. e1006006, 2016.PDF icon WenEtAl-PLoSGenetics2016.pdf (2.11 MB)
J. Zhu, Wen, D., Yu, Y., Meudt, H., and Nakhleh, L., Bayesian inference of phylogenetic networks from bi-allelic genetic markers, PLoS Computational Biology, vol. 14, no. 1, p. e1005932, 2018.PDF icon ZhuEtAl-PLoSCB18.pdf (10.6 MB)
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)
Conference Proceedings
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)
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)
N. Berestovsky, Fukui, R., and Nakhleh, L., On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks., Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. pp. 184-191, 2012.PDF icon BerestovskyFukuiNakhleh.pdf (2.77 MB)
R. A. L. Elworth and Nakhleh, L., Inferring local genealogies on closely related genomes, RECOMB Comparative Genomics, vol. LNBI 10562. pp. 213-231, 2017.PDF icon ElworthNakhleh-RECOMBCG17.pdf (2.81 MB)
Y. Yu and Nakhleh, L., A Distance-based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting, International Symposium on Bioinformatics Research and Applications (ISBRA), vol. Lecture Notes in Bioinformatics 9096. pp. 378-389, 2015.PDF icon YuNakhleh-ISBRA15.pdf (327.21 KB)
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)
Y. Yu, Warnow, T., and Nakhleh, L., Algorithms for MDC-based multi-locus phylogeny inference, The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), vol. LNBI 6577. Lecture Notes in Bioinformatics, pp. 531-545, 2011.PDF icon YuWarnowNakhleh-RECOMB11.pdf (369.65 KB)
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)
Conference Paper
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)
L. Nakhleh, Sun, J., Warnow, T., Linder, R., Moret, B. M. E., and Tholse, A., Towards the development of tools for evaluating phylogenetic network reconstruction methods, in Proc.\ 8th Pacific Symp. on Biocomputing ({PSB03}), 2003, pp. 315–326.
D. Ruths and Nakhleh, L., Techniques for Assessing Phylogenetic Branch Support: A Performance Study, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 187-196.
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.
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, 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.
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, 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.

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