Biblio

Conference Paper
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, 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.
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.
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.
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.
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.
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.
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)
Conference Proceedings
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)
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)
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 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 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)
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)
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)
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)
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)
Journal Article
Y. Yu, Warnow, T., and Nakhleh, L., “Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles”, Journal of Computational Biology, vol. 18, no. 11, pp. 1543-1559, 2011.PDF icon YuWarnowNakhleh-JCB11.pdf (419.4 KB)
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)
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)
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)
T. Ruths and Nakhleh, L., “Boosting forward-time population genetic simulators through genotype compression”, BMC Bioinformatics, vol. 14, p. 192, 2013.PDF icon RuthsNakhleh-BMCBioinfo13.pdf (680.55 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)
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)
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)

Pages