Biblio

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Book Chapter
R. A. L. Elworth, Ogilvie, H. A., Zhu, J., and Nakhleh, L., “Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization”, in Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, vol. 29, Cham: Springer, 2019.PDF icon ElworthZhuOgilvieNakhleh.pdf (743.9 KB)
Conference Paper
M. Edrisi, Zafar, H., and Nakhleh, L., “A Combinatorial Approach for Single-cell Vairant Detection via Phylogenetic Inference”, in Workshop on Algorithms in Bioinformatics (WABI), 2019.PDF icon EdrisiEtAl-WABI19.pdf (2.03 MB)
C. Than, Ruths, D., Innan, H., and Nakhleh, L., “Identifiability issues in phylogeny-based detection of horizontal gene transfer”, in Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop, 2006, vol. 4205, pp. 215-219.
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.
Conference Proceedings
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)
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)
Journal Article
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)
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.
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)
T. Warnow, Evans, S. N., Ringe, D., and Nakhleh, L., “A Stochastic model of language evolution that incorporates homoplasy and borrowing”, Phylogenetic Methods and the Prehistory of Languages, 2004.