(Q38674649)

http://europepmc.org/abstract/PMC/5510538

3 March 2018

title

Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions (English)

1 reference

http://europepmc.org/abstract/PMC/5510538

3 March 2018

0 references

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

author name string

Fei Deng

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

Sharon Aviran

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

publication date

30 March 2017

1 reference

http://europepmc.org/abstract/PMC/5510538

3 March 2018

published in

Quantitative biology (Beijing, China)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

volume

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

page(s)

3-24

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1007/s40484-017-0093-6

5 June 2020

exact match

0 references

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Comparison of SHAPE reagents for mapping RNA structures inside living cells

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23 June 2018

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Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments

23 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

23 June 2018

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23 June 2018

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Bridging the gap between in vitro and in vivo RNA folding

23 June 2018

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SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.

23 June 2018

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Metrics for rapid quality control in RNA structure probing experiments

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Data-directed RNA secondary structure prediction using probabilistic modeling

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Global Mapping of Human RNA-RNA Interactions

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Predicting RNA secondary structures from sequence and probing data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

New insights from cluster analysis methods for RNA secondary structure prediction

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Decoding the RNA structurome.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Detection of RNA-Protein Interactions in Living Cells with SHAPE.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

SHAPE directed RNA folding

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA structure: merging chemistry and genomics for a holistic perspective

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

High-throughput determination of RNA structure by proximity ligation

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

The potential of the riboSNitch in personalized medicine

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Toward a next-generation atlas of RNA secondary structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Structural imprints in vivo decode RNA regulatory mechanisms

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Improving RNA secondary structure prediction with structure mapping data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Computational analysis of RNA structures with chemical probing data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Rational experiment design for sequencing-based RNA structure mapping

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA-guided assembly of Rev-RRE nuclear export complexes

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Insights into RNA structure and function from genome-wide studies

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Landscape and variation of RNA secondary structure across the human transcriptome

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

SHAPE-Seq: High-Throughput RNA Structure Analysis

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Integrating chemical footprinting data into RNA secondary structure prediction

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Genome-wide measurement of RNA folding energies

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Evaluating our ability to predict the structural disruption of RNA by SNPs

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Reducing ligation bias of small RNAs in libraries for next generation sequencing

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

The mechanisms of RNA SHAPE chemistry

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

23 June 2018

ViennaRNA Package 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A two-dimensional mutate-and-map strategy for non-coding RNA structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Understanding the transcriptome through RNA structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Modeling and automation of sequencing-based characterization of RNA structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Improving RNA-Seq expression estimates by correcting for fragment bias

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Riboswitches and the RNA world

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Genome-wide measurement of RNA secondary structure in yeast

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Folding and Finding RNA Secondary Structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

SHAPE-directed RNA secondary structure prediction

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Advances in RNA structure analysis by chemical probing

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNAstructure: software for RNA secondary structure prediction and analysis

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Improved RNA secondary structure prediction by maximizing expected pair accuracy

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

VARNA: Interactive drawing and editing of the RNA secondary structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

23 June 2018

The centrality of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Long non-coding RNAs: insights into functions

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Accurate SHAPE-directed RNA structure determination

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNAalifold: improved consensus structure prediction for RNA alignments

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Mapping and quantifying mammalian transcriptomes by RNA-Seq

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

DMS footprinting of structured RNAs and RNA-protein complexes

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Bridging the gap in RNA structure prediction.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

CONTRAfold: RNA secondary structure prediction without physics-based models

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Prediction of RNA secondary structure by free energy minimization

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Predicting RNA pseudoknot folding thermodynamics

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Mapping nucleic acid structure by hydroxyl radical cleavage

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

How do RNA folding algorithms work?

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A comprehensive comparison of comparative RNA structure prediction approaches

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

MicroRNAs: small RNAs with a big role in gene regulation

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Alignment of RNA base pairing probability matrices

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A statistical sampling algorithm for RNA secondary structure prediction

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Pfold: RNA secondary structure prediction using stochastic context-free grammars

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Finding the common structure shared by two homologous RNAs.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Development of hammerhead ribozymes to modulate endogenous gene expression for functional studies.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

The accuracy of ribosomal RNA comparative structure models

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Secondary structure prediction for aligned RNA sequences

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA pseudoknot prediction in energy-based models

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Comparative sequence analysis and patterns of covariation in RNA secondary structures

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A dynamic programming algorithm for RNA structure prediction including pseudoknots

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Finding the most significant common sequence and structure motifs in a set of RNA sequences

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

RNA sequence analysis using covariance models

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Stochastic context-free grammars for tRNA modeling

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A critical discussion of intraclass correlation coefficients

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Fast algorithm for predicting the secondary structure of single-stranded RNA

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

On finding all suboptimal foldings of an RNA molecule

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Probing the structure of RNAs in solution

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

All oxygens in nucleic acids react with carcinogenic ethylating agents

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

3S: shotgun secondary structure determination of long non-coding RNAs.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Local RNA base pairing probabilities in large sequences.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Lead(II) cleavage analysis of RNase P RNA in vivo

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5510538

Fast folding and comparison of RNA secondary structures

31 August 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

The Estimation of the Lorenz Curve and Gini Index

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

Automated modeling of RNA 3D structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

The determination of RNA folding nearest neighbor parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

RNA secondary structures and their prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

UNAFold: software for nucleic acid folding and hybridization

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

Structural Analysis using SHALiPE to Reveal RNA G-Quadruplex Formation in Human Precursor MicroRNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS40484-017-0093-6

Enzymatic approaches to probing of RNA secondary and tertiary structure

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28717530

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A new theoretical index of biochemical reactivity combining steric and electrostatic factors. An application to yeast tRNAPhe

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28717530

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Aerial view of the HIV genome

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28717530

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S40484-017-0093-6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

journals/quanbio/ChoudharyDA17

5 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28717530%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

PubMed publication ID

28717530

1 reference