In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation

(2018) Yan Zhang et al.   MOLECULAR CELL

Principles for targeting RNA with drug-like small molecules

(2018) Katherine Deigan Warner et al.   NATURE REVIEWS DRUG DISCOVERY

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

(2018) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Economic burden of seasonal influenza in the United States

(2018) Wayan C.W.S. Putri et al.   VACCINE

Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication

(2018) Graham D. Williams et al.   Nature Communications

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tricked or trapped—Two decoy mechanisms in host–pathogen interactions

(2018) Judith K. Paulus et al.   PLoS Pathogens

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

Baloxavir Marboxil for Uncomplicated Influenza in Adults and Adolescents

(2018) Frederick G. Hayden et al.   NEW ENGLAND JOURNAL OF MEDICINE

Non-Uniform and Non-Random Binding of Nucleoprotein to Influenza A and B Viral RNA

(2018) Valerie Le Sage et al.   Viruses-Basel

A Massively Parallel Selection of Small Molecule-RNA Motif Binding Partners Informs Design of an Antiviral from Sequence

(2018) Jessica L. Childs-Disney et al.   Chem

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

(2017) Kyle E Watters et al.   NUCLEIC ACIDS RESEARCH

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

(2017) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of influenza viral RNA and nucleoprotein association

(2017) Nara Lee et al.   NUCLEIC ACIDS RESEARCH

The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications

(2017) Danny Incarnato et al.   TRENDS IN BIOTECHNOLOGY

Structural insights into RNA synthesis by the influenza virus transcription-replication machine

(2017) Alexander Pflug et al.   VIRUS RESEARCH

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

(2016) Nathan Pirakitikulr et al.   MOLECULAR CELL

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

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

(2016) Elena Rivas et al.   NATURE METHODS

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis

(2016) Aartjan J. W. te Velthuis et al.   NATURE REVIEWS MICROBIOLOGY

Reassortment in segmented RNA viruses: mechanisms and outcomes

(2016) Sarah M. McDonald et al.   NATURE REVIEWS MICROBIOLOGY

Role of mRNA structure in the control of protein folding

(2016) Guilhem Faure et al.   NUCLEIC ACIDS RESEARCH

Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production

(2016) Yuki Kobayashi et al.   RNA Biology

Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

(2016) Tri C. Nguyen et al.   Nature Communications

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

Structural Features of a 3′ Splice Site in Influenza A

(2015) Jonathan L. Chen et al.   BIOCHEMISTRY

The Influenza A PB1-F2 and N40 Start Codons Are Contained within an RNA Pseudoknot

(2015) Salvatore F. Priore et al.   BIOCHEMISTRY

Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions

(2015) Jin Chen et al.   CELL

In silico discovery and modeling of non-coding RNA structure in viruses

(2015) Walter N. Moss et al.   METHODS

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation

(2015) Marta Soszynska-Jozwiak et al.   PLoS One

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

(2015) Cristian Del Campo et al.   PLoS Genetics

Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

(2014) Tian Jiang et al.   BIOCHEMISTRY

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Secondary Structure of a Conserved Domain in the Intron of Influenza A NS1 mRNA

(2013) Salvatore F. Priore et al.   PLoS One

Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus

(2013) A. York et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

(2012) Pablo Cordero et al.   BIOCHEMISTRY

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin

(2012) Walter N. Moss et al.   PLoS One

Interaction network linking the human H3N2 influenza A virus genomic RNA segments

(2012) Emilie Fournier et al.   VACCINE

Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus

(2012) Takeshi Noda et al.   Nature Communications

ViennaRNA Package 2.0

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

A supramolecular assembly formed by influenza A virus genomic RNA segments

(2011) Emilie Fournier et al.   NUCLEIC ACIDS RESEARCH

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) W. N. Moss et al.   RNA

Cellular targets for influenza drugs

(2010) Ji-Young Min et al.   NATURE BIOTECHNOLOGY

Generation of Recombinant Influenza Virus from Plasmid DNA

(2010) Luis Martínez-Sobrido et al.   Jove-Journal of Visualized Experiments

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Influenza Virus Resistance to Antiviral Agents: A Plea for Rational Use

(2009) Gregory A. Poland et al.   CLINICAL INFECTIOUS DISEASES

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

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