Structural divergence creates new functional features in alphavirus genomes

Ablation of Programmed −1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity

(2016) Joseph A. Kendra et al.   JOURNAL OF VIROLOGY

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution

(2016) Katrina M. Kutchko et al.   Wiley Interdisciplinary Reviews-RNA

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Multiple conformations are a conserved and regulatory feature of theRB15′ UTR

(2015) Katrina M. Kutchko et al.   RNA

The 5′ and 3′ ends of alphavirus RNAs – Non-coding is not non-functional

(2015) Jennifer L. Hyde et al.   VIRUS RESEARCH

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

(2014) David Loughrey et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

A Viral RNA Structural Element Alters Host Recognition of Nonself RNA

(2014) J. L. Hyde et al.   SCIENCE

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments

(2013) Ruslan A. Soldatov et al.   BIOINFORMATICS

Functional Characterization of the Alphavirus TF Protein

(2013) J. E. Snyder et al.   JOURNAL OF VIROLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Computational identification of functional RNA homologs in metagenomic data

(2013) Eric P. Nawrocki et al.   RNA Biology

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

(2013) Justin Ritz et al.   PLoS Computational Biology

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

(2013) Elizabeth Pollom et al.   PLoS Pathogens

Alphaviruses: Population genetics and determinants of emergence

(2012) Scott C. Weaver et al.   ANTIVIRAL RESEARCH

Arthritogenic alphaviruses—an overview

(2012) Andreas Suhrbier et al.   Nature Reviews Rheumatology

Eilat virus, a unique alphavirus with host range restricted to insects by RNA replication

(2012) F. Nasar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An attenuating mutation in a neurovirulent Sindbis virus strain interacts with the IPS-1 signaling pathway in vivo

(2012) Amy C. Wollish et al.   VIROLOGY

Genome-Scale Phylogeny of the Alphavirus Genus Suggests a Marine Origin

(2011) N. L. Forrester 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

Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element

(2011) Andrew E. Firth et al.   NUCLEIC ACIDS RESEARCH

Sharing and archiving nucleic acid structure mapping data

(2011) P. Rocca-Serra et al.   RNA

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

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

(2009) Joseph M. Watts et al.   NATURE

The nsP3 macro domain is important for Sindbis virus replication in neurons and neurovirulence in mice

(2009) Eunhye Park et al.   VIROLOGY

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma

(2008) Andrew E Firth et al.   Virology Journal

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

(2008) Kevin A Wilkinson et al.   PLOS BIOLOGY