Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

(2021) Nicholas C. Huston et al.   MOLECULAR CELL

In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs

(2021) Lei Sun et al.   CELL

Challenges in ensuring global access to COVID-19 vaccines: production, affordability, allocation, and deployment

(2021) Olivier J Wouters et al.   LANCET

The time to offer treatments for COVID-19

(2021) Binh T. Ngo et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

(2021) Pramod R. Bhatt et al.   SCIENCE

Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

(2021) Kaiming Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Restriction of SARS-CoV-2 replication by targeting programmed −1 ribosomal frameshifting

(2021) Yu Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions

(2021) Siwy Ling Yang et al.   Nature Communications

Structural dynamics of single SARS-CoV-2 pseudoknot molecules reveal topologically distinct conformers

(2021) Krishna Neupane et al.   Nature Communications

Covid-19: Pfizer’s paxlovid is 89% effective in patients at risk of serious illness, company reports

(2021) Elisabeth Mahase   BMJ-British Medical Journal

Covid-19: Molnupiravir reduces risk of hospital admission or death by 50% in patients at risk, MSD reports

(2021) Elisabeth Mahase   BMJ-British Medical Journal

Genomic variance of the 2019‐nCoV coronavirus

(2020) Carmine Ceraolo et al.   JOURNAL OF MEDICAL VIROLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

(2020) Phillip J. Tomezsko et al.   NATURE

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look

(2020) Ramya Rangan et al.   RNA

Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)

(2020) Jamie A. Kelly et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

(2020) Abhik K. Banerjee et al.   CELL

The coding capacity of SARS-CoV-2

(2020) Yaara Finkel et al.   NATURE

Secondary structure of the SARS-CoV-2 5’-UTR

(2020) Zhichao Miao et al.   RNA Biology

Targeting the SARS-CoV-2 RNA Genome with Small Molecule Binders and Ribonuclease Targeting Chimera (RIBOTAC) Degraders

(2020) Hafeez S. Haniff et al.   ACS Central Science

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

(2020) Omer Ziv et al.   MOLECULAR CELL

RNApdbee 2.0: multifunctional tool for RNA structure annotation

(2018) Tomasz Zok et al.   NUCLEIC ACIDS RESEARCH

Structural and functional conservation of cis -acting RNA elements in coronavirus 5'-terminal genome regions

(2018) Ramakanth Madhugiri et al.   VIROLOGY

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Structural Analysis of Multi-Helical RNAs by NMR–SAXS/WAXS: Application to the U4/U6 di-snRNA

(2016) Gabriel Cornilescu et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication

(2015) Chringma Sherpa et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The structure and functions of coronavirus genomic 3′ and 5′ ends

(2015) Dong Yang et al.   VIRUS RESEARCH

Continuous and Discontinuous RNA Synthesis in Coronaviruses

(2015) Isabel Sola et al.   Annual Review of Virology

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

(2013) Silvi Rouskin et al.   NATURE

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mouse Hepatitis Virus Stem-Loop 4 Functions as a Spacer Element Required To Drive Subgenomic RNA Synthesis

(2011) D. Yang et al.   JOURNAL OF VIROLOGY

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins

(2010) E. P. Plant et al.   JOURNAL OF VIROLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The role of programmed-1 ribosomal frameshifting in coronavirus propagation

(2008) Ewan et al.   Frontiers in Bioscience-Landmark

Structural Lability in Stem–Loop 1 Drives a 5′ UTR–3′ UTR Interaction in Coronavirus Replication

(2008) Lichun Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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