FRESCo: finding regions of excess synonymous constraint in diverse viruses

Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses

(2014) Andrew E. Firth   NUCLEIC ACIDS RESEARCH

Synonymous site conservation in the HIV-1 genome

(2013) Itay Mayrose et al.   BMC EVOLUTIONARY BIOLOGY

Global RNA Structure Analysis of Poliovirus Identifies a Conserved RNA Structure Involved in Viral Replication and Infectivity

(2013) C. P. Burrill et al.   JOURNAL OF VIROLOGY

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design

(2012) Y. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

(2011) M. F. Lin et al.   GENOME RESEARCH

A New Ebola Virus Nonstructural Glycoprotein Expressed through RNA Editing

(2011) M. Mehedi et al.   JOURNAL OF VIROLOGY

Conservation of a Packaging Signal and the Viral Genome RNA Packaging Mechanism in Alphavirus Evolution

(2011) D. Y. Kim et al.   JOURNAL OF VIROLOGY

Detection of a Fourth Orbivirus Non-Structural Protein

(2011) Mourad Belhouchet et al.   PLoS One

Virus-encoded microRNAs

(2011) Adam Grundhoff et al.   VIROLOGY

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis -acting functions

(2010) Wilson Li et al.   NUCLEIC ACIDS RESEARCH

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

NS1' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness

(2009) E. B. Melian et al.   JOURNAL OF VIROLOGY

Evolutionary Fingerprinting of Genes

(2009) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

(2009) Andrew E Firth et al.   Virology Journal

An overlapping essential gene in the Potyviridae

(2008) B. Y.-W. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis

(2008) Karen Clyde et al.   VIROLOGY

Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

(2008) Andrew E Firth   Virology Journal