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

Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells

(2019) Arnab Sengupta et al.   PLOS BIOLOGY

The roles of five conserved lentiviral RNA structures in HIV-1 replication

(2018) Yang Liu et al.   VIROLOGY

Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication

(2018) Matthew A. Takata et al.   PLoS Pathogens

Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping

(2018) Siqi Tian et al.   eLife

Characterizing HIV-1 Splicing by Using Next-Generation Sequencing

(2017) Ann Emery et al.   JOURNAL OF VIROLOGY

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

(2017) Aleksandar Spasic 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

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

(2016) Meghan Zubradt et al.   NATURE METHODS

Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions

(2015) Natalia N. Singh et al.   Annals of the New York Academy of Sciences

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

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

(2015) Yasushi Kondo et al.   eLife

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

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

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

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

(2013) Silvi Rouskin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

(2012) Karen E. Ocwieja et al.   NUCLEIC ACIDS RESEARCH

Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms

(2011) Jean-François Lemay et al.   PLoS Genetics

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

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

Role of RNA structure in regulating pre-mRNA splicing

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

Conserved RNA secondary structures promote alternative splicing

(2008) P. J. Shepard et al.   RNA