Recent Submissions

  • Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data 

    Bao, Le, Hong Gu, Katherine A. Dunn, and Joseph P. Bielawski. 2007. "Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data." Bmc Evolutionary Biology 7: 5-S5.
    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 

    Ward, Todd J., Thomas F. Ducey, Thomas Usgaard, Katherine A. Dunn, et al. 2008. "Multilocus Genotyping Assays for Single Nucleotide Polymorphism-Based Subtyping of Listeria monocytogenes Isolates." Applied and Environmental Microbiology 74(24): 7629-7642.
    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 

    Anisimova, Maria, Joseph Bielawski, Katherine Dunn, and Ziheng Yang. 2007. "Phylogenomic analysis of natural selection pressure in Streptococcus genomes." Bmc Evolutionary Biology 7: 154-154.
    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 

    Sullivan, Matthew B., Debbie Lindell, Jessica A. Lee, Luke R. Thompson, et al. 2006. "Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts." Plos Biology 4(8): 1344-1357.
    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 ...
  • Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices 

    Dunn, Katherine A., Wenyi Jiang, Christopher Field, and Joseph P. Bielawski. 2013. "Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices." Plos One 8(1): 55816-e55816.
    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 ...
  • Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon 

    Garvin, Michael R., Joseph P. Bielawski, and Anthony J. Gharrett. 2011. "Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon." Plos One 6(9): 24127-e24127.
    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 ...