Tomas Vinar, Brona Brejova, Giltae Song, Adam C. Siepel. Reconstructing Histories of Complex Gene Clusters on a Phylogeny. Journal of Computational Biology, 17(9):1267-1279. 2010. Early version appeared in RECOMB-CG 2009.

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Clusters of genes that have evolved by repeated segmental
duplication present difficult challenges throughout genomic analysis, from
sequence assembly to functional analysis. These clusters are one of the
major sources of evolutionary innovation, and they are linked to multiple
diseases, including HIV and a variety of cancers. Understanding their
evolutionary histories is a key to the application of comparative genomics
methods in these regions of the genome. We propose a probabilistic model
of gene cluster evolution on a phylogeny, and an MCMC algorithm for
reconstruction of duplication histories from genomic sequences in multiple
species. Several projects are underway to obtain high quality BAC-based
assemblies of duplicated clusters in multiple species, and we anticipate
use of our methods in their analysis.