Biblio

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2020
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)
2019
G. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., “Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics”, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 MB)
G. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., “Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics”, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 MB)
G. A. Bravo, Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F. P., Wiedenhoeft, J., .Willows-Munro, S., and Edwards, S. V., “Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics”, PeerJ, vol. 7, p. e6399, 2019.PDF icon PeerJ2019.pdf (3.72 MB)
2018
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 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)
D. Wen, Yu, Y., Zhu, J., and Nakhleh, L., “Inferring phylogenetic networks using PhyloNet”, Systematic Biology, vol. 67, no. 4, pp. 735-740, 2018.PDF icon phylonet3.pdf (144.21 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)
2016
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)
H. Zafar, Wang, Y., Nakhleh, L., Navin, N., and Chen, K., “Monovar: single nucleotide variant detection in single cells”, Nature Methods, vol. 13, no. 6, pp. 505-507, 2016.PDF icon ZafarEtAl-NMETH2016.pdf (1.51 MB)
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)
2013
F. Barbancon, Evans, S., Nakhleh, L., Ringe, D., and Warnow, T., “An experimental study comparing linguistic phylogenetic reconstruction methods”, Diachronica, vol. 30, no. 2, pp. 143-170, 2013.PDF icon Diachronica13.pdf (575.02 KB)
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)
2011
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)
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)
2005
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.
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.
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.
L. Nakhleh and Wang, L. S., “Phylogenetic networks, trees, and clusters”, in Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA 05), 2005, vol. 3515, pp. 919-926.
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.
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, 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.
2004
C. R. Linder, Moret, B. M. E., Nakhleh, L., and Warnow, T., “Network (reticulate) evolution: biology, models, and algorithms”, in The Ninth Pacific Symposium on Biocomputing (PSB), 2004.
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, 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.

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