Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors

RNA stabilization by a poly(A) tail 3ʹ-end binding pocket and other modes of poly(A)-RNA interaction

(2021) Seyed-Fakhreddin Torabi et al.   SCIENCE

RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing

(2019) Heidi Dvinge et al.   GENOME RESEARCH

Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures

(2019) Hazrina Yusof Hamdani et al.   Crystals

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

(2018) Vladimir Reinharz et al.   NUCLEIC ACIDS RESEARCH

Riboswitches and Translation Control

(2018) Ronald R. Breaker   Cold Spring Harbor Perspectives in Biology

URS DataBase: universe of RNA structures and their motifs

(2016) Eugene Baulin et al.   Database-The Journal of Biological Databases and Curation

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

(2015) Peter Kerpedjiev et al.   BIOINFORMATICS

DSSR: an integrated software tool for dissecting the spatial structure of RNA

(2015) Xiang-Jun Lu et al.   NUCLEIC ACIDS RESEARCH

Novel features for identifying A-minors in three-dimensional RNA molecules

(2013) Palak Sheth et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

An RNA folding motif: GNRA tetraloop–receptor interactions

(2013) Julie L. Fiore et al.   QUARTERLY REVIEWS OF BIOPHYSICS

R- chie : a web server and R package for visualizing RNA secondary structures

(2012) Daniel Lai et al.   NUCLEIC ACIDS RESEARCH

Structural Variation and Uniformity among Tetraloop-Receptor Interactions and Other Loop-Helix Interactions in RNA Crystal Structures

(2012) Li Wu et al.   PLoS One

Riboswitch control of Rho-dependent transcription termination

(2012) K. Hollands et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding the Sequence Preference of Recurrent RNA Building Blocks Using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

(2011) Arnošt Mládek et al.   Journal of Chemical Theory and Computation

Non-coding RNAs: Meet thy masters

(2010) Fabrício F. Costa   BIOESSAYS

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Promoting RNA helical stacking via A-minor junctions

(2010) Cody Geary et al.   NUCLEIC ACIDS RESEARCH

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Sensitivity Analysis of k-Fold Cross Validation in Prediction Error Estimation

(2009) J.D. Rodriguez et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Classification and energetics of the base-phosphate interactions in RNA

(2009) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

Riboswitches: Emerging Themes in RNA Structure and Function

(2008) Rebecca K. Montange et al.   Annual Review of Biophysics

Annotation of tertiary interactions in RNA structures reveals variations and correlations

(2008) Y. Xin et al.   RNA