Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage

Nucleotide composition of the Zika virus RNA genome and its codon usage

(2016) Formijn van Hemert et al.   Virology Journal

Different patterns of codon usage in the overlapping polymerase and surface genes of hepatitis B virus suggest a de novo origin by modular evolution

(2015) Angelo Pavesi   JOURNAL OF GENERAL VIROLOGY

Nucleotide sequence conservation in paramyxoviruses; the concept of codon constellation

(2015) Bert K. Rima   JOURNAL OF GENERAL VIROLOGY

Sequence-specific activation of the DNA sensor cGAS by Y-form DNA structures as found in primary HIV-1 cDNA

(2015) Anna-Maria Herzner et al.   NATURE IMMUNOLOGY

Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

(2015) Zsuzsanna Sükösd et al.   NUCLEIC ACIDS RESEARCH

Functionally conserved architecture of hepatitis C virus RNA genomes

(2015) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Importance of codon usage for the temporal regulation of viral gene expression

(2015) Young C. Shin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the biased nucleotide composition of the human coronavirus RNA genome

(2015) Ben Berkhout et al.   VIRUS RESEARCH

Genome-wide analysis of codon usage bias in Ebolavirus

(2015) Juan Cristina et al.   VIRUS RESEARCH

Controlling translation via modulation of tRNA levels

(2015) Jeremy E. Wilusz   Wiley Interdisciplinary Reviews-RNA

Global Changes in the RNA Binding Specificity of HIV-1 Gag Regulate Virion Genesis

(2014) Sebla B. Kutluay et al.   CELL

Comparative mutational analyses of influenza A viruses

(2014) Peter Pak-Hang Cheung et al.   RNA

On the nucleotide composition and structure of retroviral RNA genomes

(2014) Formijn van Hemert et al.   VIRUS RESEARCH

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

(2014) Edgar E. Lara-Ramírez et al.   Biomed Research International

A detailed comparative analysis on the overall codon usage patterns in West Nile virus

(2013) Gonzalo Moratorio et al.   INFECTION GENETICS AND EVOLUTION

Reply to “Codon Usage Frequency of RNA Virus Genomes from High-Temperature Acidic-Environment Metagenomes”

(2013) Mark Young et al.   JOURNAL OF VIROLOGY

Causes and Implications of Codon Usage Bias in RNA Viruses

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

The Distribution of Synonymous Codon Choice in the Translation Initiation Region of Dengue Virus

(2013) Jian-hua Zhou et al.   PLoS One

Approaches to define the viral genetic basis of classical swine fever virus virulence

(2013) Immanuel Leifer et al.   VIROLOGY

A Comparison of Synonymous Codon Usage Bias Patterns in DNA and RNA Virus Genomes: Quantifying the Relative Importance of Mutational Pressure and Natural Selection

(2013) Youhua Chen   Biomed Research International

Analysis of base and codon usage by rubella virus

(2012) Yumei Zhou et al.   ARCHIVES OF VIROLOGY

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11

(2012) Manqing Li et al.   NATURE

Genomic HIV RNA Induces Innate Immune Responses through RIG-I-Dependent Sensing of Secondary-Structured RNA

(2012) Randi K. Berg et al.   PLoS One

The Biased Nucleotide Composition of HIV-1 Triggers Type I Interferon Response and Correlates with Subtype D Increased Pathogenicity

(2012) Nicolas Vabret et al.   PLoS One

The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

(2012) Antoinette C van der Kuyl et al.   Retrovirology

The A-nucleotide preference of HIV-1 in the context of its structured RNA genome

(2012) Formijn J. van Hemert et al.   RNA Biology

Organization of the Influenza Virus Replication Machinery

(2012) A. Moeller et al.   SCIENCE

Selective pressure dominates the synonymous codon usage in parvoviridae

(2012) Sheng-Lin Shi et al.   VIRUS GENES

The characteristic of codon usage pattern and its evolution of hepatitis C virus

(2011) Jin-song Hu et al.   INFECTION GENETICS AND EVOLUTION

HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency

(2011) A. van Weringh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of codon usage in bovine viral diarrhea virus

(2010) Meng Wang et al.   ARCHIVES OF VIROLOGY

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

(2010) Emily HM Wong et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of the sequence composition of Flaviviruses

(2009) Alyxandria M. Schubert et al.   INFECTION GENETICS AND EVOLUTION

Categorizing Host-Dependent RNA Viruses by Principal Component Analysis of Their Codon Usage Preferences

(2009) Ming-Wei Su et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

(2009) Iris Bahir et al.   Molecular Systems Biology

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts

(2008) Alessandra Carbone   JOURNAL OF MOLECULAR EVOLUTION

Bioinformatic and Physical Characterizations of Genome-Scale Ordered RNA Structure in Mammalian RNA Viruses

(2008) M. Davis et al.   JOURNAL OF VIROLOGY

Analysis of synonymous codon usage in classical swine fever virus

(2008) Pan Tao et al.   VIRUS GENES