Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla –selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses

Causes and Implications of Codon Usage Bias in RNA Viruses

(2013) Ilya S. Belalov et al.   PLoS One

Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

(2012) Jean Bérard et al.   SYSTEMATIC BIOLOGY

DNA methylation in insects: on the brink of the epigenomic era

(2011) K. M. Glastad et al.   INSECT MOLECULAR BIOLOGY

Target Cell-Mediated Editing of HIV-1 cDNA by APOBEC3 Proteins in Human Macrophages

(2011) F. A. Koning et al.   JOURNAL OF VIROLOGY

Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral

(2011) Charles E. Samuel   VIROLOGY

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons

(2009) C. C. Burns et al.   JOURNAL OF VIROLOGY

Patterns of Oligonucleotide Sequences in Viral and Host Cell RNA Identify Mediators of the Host Innate Immune System

(2009) Benjamin D. Greenbaum et al.   PLoS One

Virus-Host Coevolution: Common Patterns of Nucleotide Motif Usage in Flaviviridae and Their Hosts

(2009) Francisco P. Lobo et al.   PLoS One

Pitfalls of the most commonly used models of context dependent substitution

(2008) Helen Lindsay et al.   Biology Direct

Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals

(2008) Martin W. Simmen   GENOMICS

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses

(2008) Benjamin D. Greenbaum et al.   PLoS Pathogens