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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.