Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses

Large-Scale Nucleotide Optimization of Simian Immunodeficiency Virus Reduces Its Capacity To Stimulate Type I Interferon In Vitro

(2014) N. Vabret et al.   JOURNAL OF VIROLOGY

Evolutionary Dynamics of Restriction Site Avoidance

(2012) Long Qian et al.   PHYSICAL REVIEW LETTERS

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

Suppression of TLR9 Immunostimulatory Motifs in the Genome of a Gammaherpesvirus

(2011) A. C. Pezda et al.   JOURNAL OF IMMUNOLOGY

Oligonucleotide Motifs That Disappear during the Evolution of Influenza Virus in Humans Increase Alpha Interferon Secretion by Plasmacytoid Dendritic Cells

(2011) S. Jimenez-Baranda et al.   JOURNAL OF VIROLOGY

HIV-1 Modulates the tRNA Pool to Improve Translation Efficiency

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

Evolutionary pressures on simple sequence repeats in prokaryotic coding regions

(2011) Wei-Hsiang Lin et al.   NUCLEIC ACIDS RESEARCH

Live attenuated influenza virus vaccines by computer-aided rational design

(2010) Steffen Mueller et al.   NATURE BIOTECHNOLOGY

Making sense of the Legendre transform

(2009) R. K. P. Zia et al.   AMERICAN JOURNAL OF PHYSICS

TLR-mediated immune activation in HIV

(2009) J. J. Chang et al.   BLOOD

The evolutionary conundrum of pathogen mimicry

(2009) Nels C. Elde et al.   NATURE REVIEWS MICROBIOLOGY

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

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

(2009) Natasha Wood et al.   PLoS Pathogens

The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus

(2009) Rachel Brower-Sinning et al.   GENOME BIOLOGY

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