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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 ...
Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices
(2013-01)
Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial
phylogenomics (comparative mitogenomics). There is wide recognition within the field that
lineage-specific aspects of ...
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 ...
Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon
(2011-09)
The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins
involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the
evolution of twelve mitochondrial ...