Biblio

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A
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.
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)
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., ALPHA: A toolkit for automated local phylogenomic analyses, Bioinformatics, vol. 34, no. 16, pp. 2848-2850, 2018.PDF icon Alpha.pdf (211.74 KB)
C
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)
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)
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.
I. A. Kanj, Nakhleh, L., and Xia, G., The compatibility of binary characters on phylogenetic networks: Complexity and parameterized algorithms, Algorithmica, vol. 51, pp. 99-128, 2008.
H. Zafar, Navin, N., Nakhleh, L., and Chen, K., Computational approaches for inferring tumor evolution from single-cell genomic data, Current Opinion in Systems Biology, vol. 7, pp. 16-25, 2017.PDF icon ZafarEtAl-Rev2017.pdf (1.34 MB)
C. Than, Ruths, D., Innan, H., and Nakhleh, L., Confounding Factors in {HGT} Detection: Statistical Error, Coalescent Effects, and Multiple Solutions, Journal of Computational Biology, vol. 14, pp. 517-535, 2007.
D
D. Ruths, Tseng, J. T., Nakhleh, L., and Ram, P. T., De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis, in Proceedings of the RECOMB Satellite Workshop on Systems Biology and Proteomics, 2007, vol. 4205, pp. 108-118.
D. Ruths and Nakhleh, L., Deriving predictive models of signaling network dynamics from qualitative experimental data, in Proceedings of the 9th Annual International Conference on Computational Systems Biology, 2010.PDF icon RuthsNakhleh-CSB2010.pdf (548.82 KB)
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., Designing Fast Converging Phylogenetic Methods, Bioinformatics, vol. 17, pp. S190–S198, 2001.
X. Fan, Xu, J., and Nakhleh, L., Detecting large indels using optical map data, in RECOMB Comparative Genomics, 2018.PDF icon FanEtAl18.pdf (2.94 MB)
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)
Z. Zhu, Liu, X., Ogilvie, H. A., and Nakhleh, L., A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data, Bioinformatics (ISMB 19 Proceedings), vol. 35, pp. i370-i378, 2019.PDF icon ZhuEtAl-ISMB19.pdf (668.97 KB)

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