Predicting RNA secondary structures from sequence and probing data (Q26750475)

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA STRAND: the RNA secondary structure and statistical analysis database

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Efficient parameter estimation for RNA secondary structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Computational approaches for RNA energy parameter estimation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Modeling and automation of sequencing-based characterization of RNA structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Local RNA base pairing probabilities in large sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNAalifold: improved consensus structure prediction for RNA alignments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA Accessibility in cubic time

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Partition function and base pairing probabilities of RNA heterodimers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Protection of ribosomal RNA from kethoxal in polyribosomes. Implication of specific sites in ribosome function

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

A partition function algorithm for interacting nucleic acid strands

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Accurate SHAPE-directed RNA structure determination

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Thermodynamic Analysis of Interacting Nucleic Acid Strands

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

CONTRAfold: RNA secondary structure prediction without physics-based models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA folding at elementary step resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Beyond energy minimization: approaches to the kinetic folding of RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Barrier Trees of Degenerate Landscapes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Improved free-energy parameters for predictions of RNA duplex stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Computational analysis of RNA structures with chemical probing data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Folding kinetics of large RNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Use of lead(II) to probe the structure of large RNA's. Conformation of the 3' terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

The computer simulation of RNA folding pathways using a genetic algorithm.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Regulation of microRNA biogenesis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Alignment of RNA base pairing probability matrices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Secondary structure prediction for aligned RNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

BarMap: RNA folding on dynamic energy landscapes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Fast folding and comparison of RNA secondary structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Prediction of locally stable RNA secondary structures for genome-wide surveys.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Accelerated probabilistic inference of RNA structure evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Single-molecule correlated chemical probing of RNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Partition function and base pairing probabilities for RNA-RNA interaction prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Genome-wide measurement of RNA secondary structure in yeast

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Murlet: a practical multiple alignment tool for structural RNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Determination of in vivo RNA structure in low-abundance transcripts.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Geometric nomenclature and classification of RNA base pairs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Probing RNA structure within living cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Lead(II) as a probe for investigating RNA structure in vivo

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

2D meets 4G: G-quadruplexes in RNA secondary structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

7 January 2021

ViennaRNA Package 2.0

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Structure and dynamics of the HIV-1 frameshift element RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA pseudoknot prediction in energy-based models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Gene regulation by riboswitches

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Memory-efficient RNA energy landscape exploration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Ribosome RNA assembly intermediates visualized in living cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. I. Reaction between N-cyclohexyl-N'-β-(4-methylmorpholinium)ethylcarbodiimide and model nucleotides

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Insights into RNA structure and function from genome-wide studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Thermodynamics of RNA-RNA binding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Chemical probes for higher-order structure in RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

High-throughput determination of RNA structure by proximity ligation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Fast and effective prediction of microRNA/target duplexes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNAstructure: software for RNA secondary structure prediction and analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

A dynamic programming algorithm for RNA structure prediction including pseudoknots

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Relationship between internucleotide linkage geometry and the stability of RNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA SHAPE analysis in living cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Pseudoknots: RNA structures with diverse functions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

An RNA folding method capable of identifying pseudoknots and base triples.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Fast accessibility-based prediction of RNA-RNA interactions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNAplex: a fast tool for RNA-RNA interaction search

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Using motion planning to study RNA folding kinetics.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Simulating RNA folding kinetics on approximated energy landscapes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Improved Estimation of Secondary Structure in Ribonucleic Acids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Estimation of Secondary Structure in Ribonucleic Acids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Multiple structural alignment and clustering of RNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Mapping nucleic acid structure by hydroxyl radical cleavage

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Genome-wide measurement of RNA folding energies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Advances in RNA structure analysis by chemical probing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Efficient computation of RNA folding dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Exploring the lower part of discrete polymer model energy landscapes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Complete suboptimal folding of RNA and the stability of secondary structures.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

NUPACK: Analysis and design of nucleic acid systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Rich parameterization improves RNA structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Integrating chemical footprinting data into RNA secondary structure prediction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

RNA folding in living cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

A folding algorithm for extended RNA secondary structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

On finding all suboptimal foldings of an RNA molecule

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.04.004