Biblio

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Epidemiology
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.
S. Takuno, Kado, T., Sugino, R. P., Nakhleh, L., and Innan, H., “Population genomics in bacteria: A case study of Staphylococcus aureus.”, Molecular Biology and Evolution, vol. 29, no. 2, pp. 797-800, 2012.PDF icon TakunoEtAl-MBE11.pdf (933.28 KB)
PhyloNet
S. Takuno, Kado, T., Sugino, R. P., Nakhleh, L., and Innan, H., “Population genomics in bacteria: A case study of Staphylococcus aureus.”, Molecular Biology and Evolution, vol. 29, no. 2, pp. 797-800, 2012.PDF icon TakunoEtAl-MBE11.pdf (933.28 KB)
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.
L. Nakhleh, Ruths, D., and Innan, H., “Gene trees, species trees, and species networks”, in Meta-analysis and Combining Information in Genetics, R. Guerra and Goldstein, D., Eds. Chapman & Hall, CRC Press, 2009, pp. 275-293.
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.
Trees
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.
L. Nakhleh, Ruths, D., and Innan, H., “Gene trees, species trees, and species networks”, in Meta-analysis and Combining Information in Genetics, R. Guerra and Goldstein, D., Eds. Chapman & Hall, CRC Press, 2009, pp. 275-293.