Advances and opportunities in RNA structure experimental determination and computational modeling

Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer

(2022) Philip Z Johnson et al.   NUCLEIC ACIDS RESEARCH

Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells

(2022) Ryan Van Damme et al.   Nature Communications

Secondary structure prediction for RNA sequences including N6-methyladenosine

(2022) Elzbieta Kierzek et al.   Nature Communications

Deep learning models for RNA secondary structure prediction (probably) do not generalize across families

(2022) Marcell Szikszai et al.   BIOINFORMATICS

Improved RNA Secondary Structure and Tertiary Base-pairing Prediction Using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning

(2021) Jaswinder Singh et al.   BIOINFORMATICS

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

(2021) Lei Sun et al.   CELL

Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

(2021) Lei Sun et al.   CELL RESEARCH

Genome-scale deconvolution of RNA structure ensembles

(2021) Edoardo Morandi et al.   NATURE METHODS

RNA secondary structure prediction using deep learning with thermodynamic integration

(2021) Kengo Sato et al.   Nature Communications

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolutionary conservation of RNA sequence and structure

(2021) Elena Rivas   Wiley Interdisciplinary Reviews-RNA

Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP

(2021) Thomas W. Christy et al.   BIOCHEMISTRY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Discovery of 17 conserved structural RNAs in fungi

(2021) William Gao et al.   NUCLEIC ACIDS RESEARCH

Geometric deep learning of RNA structure

(2021) Raphael J. L. Townshend et al.   SCIENCE

UFold: fast and accurate RNA secondary structure prediction with deep learning

(2021) Laiyi Fu et al.   NUCLEIC ACIDS RESEARCH

Estimating the power of sequence covariation for detecting conserved RNA structure

(2020) Elena Rivas et al.   BIOINFORMATICS

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

(2020) Phillip J. Tomezsko et al.   NATURE

RIC-seq for global in situ profiling of RNA–RNA spatial interactions

(2020) Zhaokui Cai et al.   NATURE

Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ

(2020) Tong Wu et al.   NATURE METHODS

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

(2020) Kalli Kappel et al.   NATURE METHODS

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds

(2020) Andrew Martin Watkins et al.   STRUCTURE

Determination of isoform-specific RNA structure with nanopore long reads

(2020) Jong Ghut Ashley Aw et al.   NATURE BIOTECHNOLOGY

RASP: an atlas of transcriptome-wide RNA secondary structure probing data

(2020) Pan Li et al.   NUCLEIC ACIDS RESEARCH

A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

(2020) Tycho Marinus et al.   NUCLEIC ACIDS RESEARCH

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle

(2019) Linyu Wang et al.   Frontiers in Genetics

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity

(2019) Chu-Xiao Liu et al.   CELL

A New Method of RNA Secondary Structure Prediction Based on Convolutional Neural Network and Dynamic Programming

(2019) Hao Zhang et al.   Frontiers in Genetics

Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies

(2019) Steven Busan et al.   BIOCHEMISTRY

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

The roles of structural dynamics in the cellular functions of RNAs

(2019) Laura R. Ganser et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

(2019) Jaswinder Singh et al.   Nature Communications

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

(2018) Anthony M. Mustoe et al.   CELL

Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate

(2018) Zhongmin Liu et al.   CELL

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

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

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

(2018) Padideh Danaee et al.   NUCLEIC ACIDS RESEARCH

Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes

(2018) Hua Li et al.   Nature Communications

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

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

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity

(2018) Pan Li et al.   Cell Host & Microbe

Higher-Order Organization Principles of Pre-translational mRNPs

(2018) Mihir Metkar et al.   MOLECULAR CELL

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

(2018) Kalli Kappel et al.   NATURE METHODS

In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)

(2018) David Mitchell et al.   RNA

Carbodiimide reagents for the chemical probing of RNA structure in cells

(2018) Peter Y. Wang et al.   RNA

The RNA Base-Pairing Problem and Base-Pairing Solutions

(2018) Zhipeng Lu et al.   Cold Spring Harbor Perspectives in Biology

A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model

(2018) Manato Akiyama et al.   Journal of Bioinformatics and Computational Biology

Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering

(2017) Yuba R. Bhandari et al.   JOURNAL OF MOLECULAR BIOLOGY

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

(2017) Aleksandar Spasic et al.   NUCLEIC ACIDS RESEARCH

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

(2017) Zhen Tan et al.   NUCLEIC ACIDS RESEARCH

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

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

DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers

(2017) Taichi Umeyama et al.   Cell Reports

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

(2016) Zhipeng Lu et al.   CELL

RNAComposer and RNA 3D structure prediction for nanotechnology

(2016) Marcin Biesiada et al.   METHODS

Predicting RNA secondary structures from sequence and probing data

(2016) Ronny Lorenz et al.   METHODS

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

Bridging the gap between in vitro and in vivo RNA folding

(2016) Kathleen A. Leamy et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

(2016) Michael F. Sloma et al.   RNA

Data-directed RNA secondary structure prediction using probabilistic modeling

(2016) Fei Deng et al.   RNA

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

(2016) B. M. Akiyama et al.   SCIENCE

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

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

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

(2015) Yang Wu et al.   NUCLEIC ACIDS RESEARCH

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

(2015) Michal J. Boniecki et al.   NUCLEIC ACIDS RESEARCH

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions

(2014) Yinghan Fu et al.   NUCLEIC ACIDS RESEARCH

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

Infernal 1.1: 100-fold faster RNA homology searches

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

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

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

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

(2013) Tomasz Puton et al.   NUCLEIC ACIDS RESEARCH

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

(2013) Elena Rivas   RNA Biology

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

ViennaRNA Package 2.0

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

Rich Parameterization Improves RNA Structure Prediction

(2011) Shay Zakov et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

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

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

(2011) E. Rivas et al.   RNA

Correlating SHAPE signatures with three-dimensional RNA structures

(2011) E. Bindewald et al.   RNA

A predictive model for secondary RNA structure using graph theory and a neural network

(2010) Denise R Koessler et al.   BMC BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Computational approaches for RNA energy parameter estimation

(2010) M. Andronescu et al.   RNA

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

(2009) Joseph M. Watts et al.   NATURE

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

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

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA