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Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data
(2007)
Background: Models of codon evolution have proven useful for investigating the strength and
direction of natural selection. In some cases, a priori biological knowledge has been used
successfully to model heterogeneous ...
Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of Listeria monocytogenes Isolates
(2008-12)
Listeria monocytogenes is responsible for serious invasive illness associated with consumption
of contaminated food and places a significant burden on public health and the agricultural economy.
We recently developed a ...
Phylogenomic analysis of natural selection pressure in Streptococcus genomes
(2007-08)
Background: In comparative analyses of bacterial pathogens, it has been common practice to
discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic
relatives (core genes), and (ii) ...
Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
(2006-08)
Cyanophages ( cyanobacterial viruses) are important agents of horizontal gene transfer among
marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some
cyanophage genomes carry and express ...