Biblio

Export 111 results:
Author Keyword Title Type [ Year(Asc)]
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)
2018
R. A. L. Elworth, Ogilvie, H. A., Zhu, J., and Nakhleh, L., “Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization”, 2018.PDF icon ElworthZhuOgilvieNakhleh.pdf (743.9 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 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)
X. Fan, Xu, J., and Nakhleh, L., “Detecting large indels using optical map data”, in RECOMB Comparative Genomics, 2018.
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)
J. Zhu and Nakhleh, L., “Inference of species phylogenies from bi-allelic markers using pseudo-likelihood”, Bioinformatics, vol. 34, pp. i376-385, 2018.PDF icon ZhuNakhleh-ISMB18.pdf (1.26 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)
B. J. Grindel, Martinez, J. R., Tellman, T. V., Harrington, D. A., Zafar, H., Nakhleh, L., Chung, L., and Farach-Carson, M. C., “Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells”, Scientific Reports, vol. 8, p. 7262, 2018.PDF icon GrindelEtAl.pdf (2.28 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). 2018.
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)
2017
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)
X. Fan, Chaisson, M., Nakhleh, L., and Chen, K., “HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies”, Genome Research, vol. 27, pp. 793-800, 2017.PDF icon Genome Res.-2017-Fan-793-800.pdf (476.55 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. Zafar, Tzen, A., Navin, N., Chen, K., and Nakhleh, L., “SiFit: A method for inferring tumor trees from single-cell sequencing data under finite-site models”, Genome Biology, vol. 18, p. 178, 2017.PDF icon ZafarEtAl-GB17.pdf (2.12 MB)
S. Kamoun, Lozano-Duran, R., and Nakhleh, L., “Stranger in a strange land: The experiences of immigrant researchers”, Genome Biology, vol. 18, p. 232, 2017.PDF icon Stranger-GB17.pdf (286.06 KB)
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)
Y. Yu, Jermaine, C., and Nakhleh, L., “Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks”, BMC Genomics, vol. 17, no. Suppl 10, p. 784, 2016.PDF icon YuJermaineNakhleh-BMCGenomics2016.pdf (965.19 KB)
J. Zhu, Yu, Y., and Nakhleh, L., “In the light of deep coalescence: Revisiting trees within networks”, BMC Bioinformatics, vol. 17, no. Suppl 14, p. 415, 2016.PDF icon ZhuYuNakhleh-BMCBioinfo2016.pdf (1.06 MB)
M. W. Hahn and Nakhleh, L., “Irrational Exuberance for Resolved Species Trees”, Evolution, vol. 70, no. 1, pp. 7-17, 2016.PDF icon HahnNakhleh2016.pdf (433.49 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)
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)
2015
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)
K. Liu, Steinberg, E., Yozzo, A., Song, Y., Kohn, M. H., and Nakhleh, L., “Interspecific introgressive origin of genomic diversity in the house mouse”, Proceedings of the National Academy of Sciences, vol. 112, no. 1, pp. 196-201, 2015.PDF icon LiuEtAl-PNAS2014.pdf (24.54 MB)

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