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C. Than and Nakhleh, L., Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences, in Estimating Species Trees: Practical and Theoretical Aspects, L. L. Knowles and Kubatko, L. S., Eds. Wiley-VCH, 2010.
C. Than and Nakhleh, L., Species tree inference by minimizing deep coalescences, PLoS Computational Biology, vol. 5, p. e1000501, 2009.
C. Than and Nakhleh, L., SPR-based tree reconciliation: Non-binary trees and multiple solutions, in Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC), 2008, pp. 251-260.
C. Than, Sugino, R., Innan, H., and Nakhleh, L., Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data, Bioinformatics, vol. 24, pp. i123-i131, 2008.
C. Than, Ruths, D., and Nakhleh, L., PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships, BMC Bioinformatics, vol. 9, p. 322, 2008.
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.
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.