Computational biology of RNA interactions (Q26852710)

main subject

computational biology

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Peter F. Stadler

2

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author name string

Christoph Dieterich

series ordinal

1

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language of work or name

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2013

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Wiley interdisciplinary reviews. RNA

published in

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volume

4

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issue

1

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page(s)

107-20

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

cites work

1 reference

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

21 January 2018

1 reference

Improved free-energy parameters for predictions of RNA duplex stability

21 January 2018

1 reference

21 January 2018

ViennaRNA Package 2.0

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Thermodynamics of RNA-RNA binding

21 January 2018

1 reference

Fast folding and comparison of RNA secondary structures

21 January 2018

1 reference

Algorithm independent properties of RNA secondary structure predictions

21 January 2018

1 reference

A statistical sampling algorithm for RNA secondary structure prediction

21 January 2018

1 reference

Secondary structure prediction for aligned RNA sequences

21 January 2018

1 reference

UNAFold: software for nucleic acid folding and hybridization

21 January 2018

1 reference

Regulation of mRNA translation and stability by microRNAs

21 January 2018

1 reference

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

21 January 2018

1 reference

Regulation and mode of action of the second small RNA activator of RpoS translation, RprA

21 January 2018

1 reference

Prediction of hybridization and melting for double-stranded nucleic acids

21 January 2018

1 reference

Partition function and base pairing probabilities of RNA heterodimers

21 January 2018

1 reference

Thermodynamic Analysis of Interacting Nucleic Acid Strands

21 January 2018

1 reference

NUPACK: Analysis and design of nucleic acid systems

21 January 2018

1 reference

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

21 January 2018

1 reference

RNAsnoop: efficient target prediction for H/ACA snoRNAs

21 January 2018

1 reference

RNA-RNA interaction prediction and antisense RNA target search.

21 January 2018

1 reference

A partition function algorithm for interacting nucleic acid strands

21 January 2018

1 reference

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

21 January 2018

1 reference

Target prediction and a statistical sampling algorithm for RNA-RNA interaction

21 January 2018

1 reference

Local RNA base pairing probabilities in large sequences.

21 January 2018

1 reference

Variations on RNA folding and alignment: lessons from Benasque.

21 January 2018

1 reference

TargetRNA: a tool for predicting targets of small RNA action in bacteria

21 January 2018

1 reference

RNApredator: fast accessibility-based prediction of sRNA targets

21 January 2018

1 reference

Fast accessibility-based prediction of RNA-RNA interactions

21 January 2018

1 reference

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

21 January 2018

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Revisiting the principles of microRNA target recognition and mode of action

21 January 2018

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Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor

21 January 2018

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Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency.

21 January 2018

1 reference

Thermodynamic Control of Small RNA-Mediated Gene Silencing

21 January 2018

1 reference

The impact of target site accessibility on the design of effective siRNAs

21 January 2018

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Designing optimal siRNA based on target site accessibility.

21 January 2018

1 reference

Desperately seeking microRNA targets

21 January 2018

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Practical Aspects of microRNA Target Prediction

21 January 2018

1 reference

Evaluation of online miRNA resources for biomedical applications.

21 January 2018

1 reference

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

21 January 2018

1 reference

Combinatorial microRNA target predictions

21 January 2018

1 reference

21 January 2018

Human MicroRNA targets

1 reference

Lost in translation: an assessment and perspective for computational microRNA target identification

21 January 2018

1 reference

New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites

21 January 2018

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Activation of gene expression by small RNA.

21 January 2018

1 reference

Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator

21 January 2018

1 reference

DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation.

21 January 2018

1 reference

RNA/DNA hybrid binding affinity determines telomerase template-translocation efficiency

21 January 2018

1 reference

Thermodynamic and kinetic modeling of transcriptional pausing

21 January 2018

1 reference

Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein.

21 January 2018

1 reference

Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions

21 January 2018

1 reference

The genomic binding sites of a noncoding RNA.

21 January 2018

1 reference

Nucleic acid hybridization: triplex stability and energetics

21 January 2018

1 reference

Prediction of the stability of DNA triplexes

21 January 2018

1 reference

An RNA folding method capable of identifying pseudoknots and base triples

21 January 2018

1 reference

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

21 January 2018

1 reference

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

21 January 2018

1 reference

A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes.

21 January 2018

1 reference

InterPro in 2011: new developments in the family and domain prediction database

21 January 2018

1 reference

Computational methods for prediction of protein-RNA interactions

21 January 2018

1 reference

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

21 January 2018

1 reference

Towards deciphering the principles underlying an mRNA recognition code

21 January 2018

1 reference

Protein-RNA and Protein-Protein Recognition by Dual KH1/2 Domains of the Neuronal Splicing Factor Nova-1

21 January 2018

1 reference

RNA sequence analysis using covariance models

21 January 2018

1 reference

Infernal 1.0: inference of RNA alignments

21 January 2018

1 reference

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins

21 January 2018

1 reference

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

21 January 2018

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Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

21 January 2018

1 reference

Structator: fast index-based search for RNA sequence-structure patterns

21 January 2018

1 reference

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model.

21 January 2018

1 reference

21 January 2018

HuR and mRNA stability

1 reference

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

21 January 2018

1 reference

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

21 January 2018

1 reference

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

21 January 2018

1 reference

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

21 January 2018

1 reference

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

21 January 2018

1 reference

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

21 January 2018

1 reference

Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.

21 January 2018

1 reference

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

21 January 2018

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In vitro selection of RNA molecules that bind specific ligands

21 January 2018

1 reference

Exploring molecular diversity with combinatorial shape libraries

21 January 2018

1 reference

Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers

21 January 2018

1 reference

Computational discovery of folded RNA domains in genomes and in vitro selected libraries

21 January 2018

1 reference

The distributions, mechanisms, and structures of metabolite-binding riboswitches

21 January 2018

1 reference

BarMap: RNA folding on dynamic energy landscapes

21 January 2018

1 reference

Challenges of ligand identification for riboswitch candidates

21 January 2018

1 reference

Design principles for riboswitch function

21 January 2018

1 reference

miRBase: integrating microRNA annotation and deep-sequencing data

21 January 2018

1 reference

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

21 January 2018

1 reference

RBPDB: a database of RNA-binding specificities

21 January 2018

1 reference

starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

21 January 2018

1 reference

doRiNA: a database of RNA interactions in post-transcriptional regulation

21 January 2018

1 reference

RNA secondary structures and their prediction

21 January 2018

1 reference

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

21 January 2018

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Sensory and regulatory RNAs in prokaryotes: a new German research focus

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1002/WRNA.1147

1 reference

Consolidated OpenCitations Corpus – April 2017

1 reference

Consolidated OpenCitations Corpus – April 2017

PubMed publication ID

23139167

1 reference

Consolidated OpenCitations Corpus – April 2017