ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

(2018) Chun Shen Lim et al.   Frontiers in Microbiology

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates

(2018) Bernhard Thiel et al.   Genes

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

(2017) Laura E. Ritchey et al.   NUCLEIC ACIDS RESEARCH

RNA2DMut: a web tool for the design and analysis of RNA structure mutations

(2017) Walter N. Moss   RNA

Visualization of RNA structure models within the Integrative Genomics Viewer

(2017) Steven Busan et al.   RNA

Functional RNA during Zika virus infection

(2017) Giel P. Göertz et al.   VIRUS RESEARCH

RNAStructuromeDB: A genome-wide database for RNA structural inference

(2017) Ryan J. Andrews et al.   Scientific Reports

Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication

(2017) Vladislav V. Khrustalev et al.   Frontiers in Cellular and Infection Microbiology

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

(2016) Gianluigi Lichinchi et al.   Cell Host & Microbe

N6 -Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

(2016) Nandan S. Gokhale et al.   Cell Host & Microbe

Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas

(2016) Qing Ye et al.   INFECTION GENETICS AND EVOLUTION

Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA Interference Machinery and Determines West Nile Virus Transmission by Culex pipiens Mosquitoes

(2016) G. P. Göertz et al.   JOURNAL OF VIROLOGY

Zika Virus Methyltransferase: Structure and Functions for Drug Design Perspectives

(2016) Bruno Coutard et al.   JOURNAL OF VIROLOGY

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease

(2016) B. M. Akiyama et al.   SCIENCE

RNA Structure Duplications and Flavivirus Host Adaptation

(2016) Sergio M. Villordo et al.   TRENDS IN MICROBIOLOGY

Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil

(2016) Claire L. Donald et al.   PLoS Neglected Tropical Diseases

Mutations Designed by Ensemble Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and Attenuate Viral Replication in Cell Culture

(2016) Tian Jiang et al.   PLoS One

ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

(2016) Amit Kumar Gupta et al.   Scientific Reports

Simple reverse genetics systems for Asian and African Zika viruses

(2016) Thérèse Atieh et al.   Scientific Reports

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

(2015) Yiliang Ding et al.   Nature Protocols

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures

(2015) Yinghan Fu et al.   PLoS One

New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation

(2015) Jeffrey S Kieft et al.   RNA Biology

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

Flavivirus RNA methylation

(2014) H. Dong et al.   JOURNAL OF GENERAL VIROLOGY

Functional long-range RNA–RNA interactions in positive-strand RNA viruses

(2014) Beth L. Nicholson et al.   NATURE REVIEWS MICROBIOLOGY

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

(2014) T. Puton et al.   NUCLEIC ACIDS RESEARCH

RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA

(2014) Erich G Chapman et al.   eLife

Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA

(2013) Walter N Moss et al.   BMC GENOMICS

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

Identifying Recombination Hot Spots in the HIV-1 Genome

(2013) R. P. Smyth et al.   JOURNAL OF VIROLOGY

Novel cis-Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization

(2013) Z.-Y. Liu et al.   JOURNAL OF VIROLOGY

Identification of cis-Acting Nucleotides and a Structural Feature in West Nile Virus 3'-Terminus RNA That Facilitate Viral Minus Strand RNA Synthesis

(2013) W. G. Davis et al.   JOURNAL OF VIROLOGY

RNAstructure: web servers for RNA secondary structure prediction and analysis

(2013) Stanislav Bellaousov et al.   NUCLEIC ACIDS RESEARCH

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

(2013) Shigehiro Kuraku et al.   NUCLEIC ACIDS RESEARCH

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Taking a cellular road-trip: mRNA transport and anchoring

(2012) Catherine A Pratt et al.   CURRENT OPINION IN CELL BIOLOGY

The regulation of mRNA stability in mammalian cells: 2.0

(2012) Xiangyue Wu et al.   GENE

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

(2012) Kourosh Zarringhalam et al.   PLoS One

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Identification of potential conserved RNA secondary structure throughout influenza A coding regions

(2011) W. N. Moss et al.   RNA

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

A balance between circular and linear forms of the dengue virus genome is crucial for viral replication

(2010) S. M. Villordo et al.   RNA

Folding and Finding RNA Secondary Structure

(2010) D. H. Mathews et al.   Cold Spring Harbor Perspectives in Biology

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

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

(2009) Joseph M. Watts et al.   NATURE

Dinucleotide controlled null models for comparative RNA gene prediction

(2008) Tanja Gesell et al.   BMC BIOINFORMATICS

A Highly Structured, Nuclease-Resistant, Noncoding RNA Produced by Flaviviruses Is Required for Pathogenicity

(2008) Gorben P. Pijlman et al.   Cell Host & Microbe

Structural and Functional Studies of the Promoter Element for Dengue Virus RNA Replication

(2008) M. F. Lodeiro et al.   JOURNAL OF VIROLOGY

Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element

(2008) D. L. Ouellet et al.   NUCLEIC ACIDS RESEARCH

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

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