Michael A. Charleston

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The processes of gene duplication, loss, and lineage sorting can result in incongruence between the phylogenies of genes and those of species. This incongruence complicates the task of inferring the latter from the former. We describe the use of reconciled trees to reconstruct the history of a gene tree with respect to a species tree. Reconciled trees allow(More)
Hepatitis C virus (HCV) is a leading worldwide cause of liver disease. Here, we use a new model of HCV spread to investigate the epidemic behavior of the virus and to estimate its basic reproductive number from gene sequence data. We find significant differences in epidemic behavior among HCV subtypes and suggest that these differences are largely the(More)
The association between two or more lineages over evolutionary time is a recurrent theme spanning several different fields within biology, from molecular evolution to coevolution and biogeography. In each `historical association', one lineage is associated with another, and can be thought of as tracking the other over evolutionary time with a greater or(More)
The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which(More)
Primate lentiviruses (PLV) from closely related primate species have been observed to be more closely related to each other than to PLV from more distantly related primate species. The current explanation for this observation is the codivergence hypothesis; that is, the divergence of a virus lineage results from the divergence of the host lineage. We show(More)
We explore model-based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the(More)
The geographical origin of Plasmodium vivax, the most widespread human malaria parasite, is controversial. Although genetic closeness to Asian primate malarias has been confirmed by phylogenetic analyses, genetic similarities between P. vivax and Plasmodium simium, a New World primate malaria, suggest that humans may have acquired P. vivax from New World(More)
MOTIVATION Current microarray analyses focus on identifying sets of genes that are differentially expressed (DE) or differentially coexpressed (DC) in different biological states (e.g. diseased versus non-diseased). We observed that in many human diseases, some genes have a significant increase or decrease in expression variability (variance). As these(More)