Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. - Cuong Than; Derek A. Ruths; Hideki Innan; Luay Nakhleh (Comparative Genomics, 2006)

Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. - Cuong Than; Derek A. Ruths; Hideki Innan; Luay Nakhleh (J. Comput. Biol., 2007)

Efficient inference of bacterial strain trees from genome-scale multilocus data. - Cuong Than; R. Sugino; Hideki Innan; Luay Nakhleh (ISMB, 2008)

mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. - Kosuke M. Teshima; Hideki Innan (BMC Bioinform., 2009)