Biblio

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Conference Paper
L. Nakhleh, Moret, B. M. E., Roshan, U., John, S. K., Sun, J., and Warnow, T., “The Accuracy of Phylogenetic Methods for Large Datasets”, in Proc.\ 7th Pacific Symp. on Biocomputing ({PSB02}), 2002, vol. 7, pp. 211-222.
L. Nakhleh, Roshan, U., Vawter, L., and Warnow, T., “Estimating the Deviation from a Molecular Clock”, in Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI 02), Rome, Italy, 2002, vol. 2452, pp. 287-299.
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.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., “The Performance of Phylogenetic Methods on Trees of Bounded Diameter”, in First International Workshop on Algorithms in Bioinformatics (WABI 01), 2001, vol. Lecture Notes in Computer Science 2149, pp. 214–226.
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, 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, 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.
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.
Conference Proceedings
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)
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)
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)
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)
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, Roshan, U., John, S. K., Sun, J., and Warnow, T., “Designing Fast Converging Phylogenetic Methods”, Bioinformatics, vol. 17, pp. S190–S198, 2001.
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)
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)
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)
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)
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)
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.

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