Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

3′ Cap-Independent Translation Enhancers of Plant Viruses

(2013) Anne E. Simon et al.   Annual Review of Microbiology

RNA Secondary Structure Prediction Using Soft Computing

(2013) Shubhra Sankar Ray et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Packaging signals in single-stranded RNA viruses: nature’s alternative to a purely electrostatic assembly mechanism

(2013) Peter G. Stockley et al.   JOURNAL OF BIOLOGICAL PHYSICS

Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland

(2013) L. Julian et al.   JOURNAL OF GENERAL VIROLOGY

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

(2013) Daniel Cardinale et al.   Viruses-Basel

DOOSS: a tool for visual analysis of data overlaid on secondary structures

(2012) Michael Golden et al.   BIOINFORMATICS

Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus

(2012) Adérito L Monjane et al.   BMC EVOLUTIONARY BIOLOGY

Coevolution in RNA Molecules Driven by Selective Constraints: Evidence from 5S rRNA

(2012) Nan Cheng et al.   PLoS One

The influenza A segment 7 mRNA 3′ splice site pseudoknot/hairpin family

(2012) Walter N. Moss et al.   RNA Biology

The HIV-1 Rev response element

(2012) Jason Fernandes et al.   RNA Biology

RNA Structural Elements of Hepatitis C Virus Controlling Viral RNA Translation and the Implications for Viral Pathogenesis

(2012) David Piñeiro et al.   Viruses-Basel

NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments

(2011) J. Y. Semegni et al.   BIOINFORMATICS

The Diversity of Torque Teno Viruses: In Vitro Replication Leads to the Formation of Additional Replication-Competent Subviral Molecules

(2011) E.-M. de Villiers et al.   JOURNAL OF VIROLOGY

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

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

Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation

(2011) Noemí Fernández et al.   NUCLEIC ACIDS RESEARCH

Complex Recombination Patterns Arising during Geminivirus Coinfections Preserve and Demarcate Biologically Important Intra-Genome Interaction Networks

(2011) Darren P. Martin et al.   PLoS Pathogens

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus

(2010) X. Zuo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Cytokine induction by immunostimulatory DNA in porcine PBMC is impaired by a hairpin forming sequence motif from the genome of Porcine Circovirus type 2 (PCV2)

(2010) F. Hasslung Wikström et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs

(2009) Anne E. Simon et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Molecular Characterization of Infectious Clones of the Minute Virus of Canines Reveals Unique Features of Bocaviruses

(2009) Y. Sun et al.   JOURNAL OF VIROLOGY

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

(2009) Joseph M. Watts et al.   NATURE

Importance of mRNA Secondary Structural Elements for the Expression of Influenza Virus Genes

(2009) Petr O. Ilyinskii et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Role of RNA structure in regulating pre-mRNA splicing

(2009) M. Bryan Warf et al.   TRENDS IN BIOCHEMICAL SCIENCES

Replication of porcine circoviruses

(2009) Florence Faurez et al.   Virology Journal

Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses

(2008) P. Lefeuvre et al.   JOURNAL OF VIROLOGY

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

(2008) Nobubelo K Ngandu et al.   Virology Journal