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Citations per year

Number of citations per year for the bioinformatics software tool RNAcontext
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This map represents all the scientific publications referring to RNAcontext per scientific context
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RNAcontext specifications

Information


Unique identifier OMICS_02253
Name RNAcontext
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_02253
Name RNAcontext
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for RNAcontext

RNAcontext citations

 (11)
library_books

Inferring RNA sequence preferences for poorly studied RNA binding proteins based on co evolution

2018
BMC Bioinformatics
PMCID: 5848454
PMID: 29529991
DOI: 10.1186/s12859-018-2091-8

[…] inding intensity for approximately 240,000 RNA probe sequences. Position frequency matrices were derived using top 10 probes for each experiment []. Many previous methods including 1NN, DeepBind, RCK/RNAcontext were all trained and tested on this dataset. We used the position frequency matrices in this dataset to form our training set, and the probes to form our in vitro testing set.We performed s […]

library_books

RNA protein binding motifs mining with a new hybrid deep learning based cross domain knowledge integration approach

2017
BMC Bioinformatics
PMCID: 5331642
PMID: 28245811
DOI: 10.1186/s12859-017-1561-8

[…] There are many computational methods developed for predicting RNA-protein binding sites. such as iONMF, Oli, DeepBind, GraphProt and RNAContext. As indicated in [], iONMF performs a little better than GraphProt, and much better than RNAContext. In []), Oli with only tetranucleotide frequency features yield better performance than i […]

library_books

Integrating Epigenomics into the Understanding of Biomedical Insight

2016
Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] aracterization. Previously developed tools for DNA and protein motif discoveries can be implemented to the RNA datasets and performed well, which include HOMER, MEME, cERMIT, GLAM2, MatrixREDUCE, and RNAcontext. Although there are tools for the ncRNA secondary structure prediction and functional annotation, such as GraphProt, CapR, and LncRNA2Function, there are still significant challenges in thi […]

library_books

Advances in the characterization of RNA‐binding proteins

2016
PMCID: 5113702
PMID: 27503141
DOI: 10.1002/wrna.1378

[…] A large number of computational methods address the problem of characterizing RNA partners of specific RBPs. MEME, RBPmap, SeAMotE, and RNAcontext identify motifs enriched in RNA targets. The use of sequence motifs allows discovery of targets in RNA datasets, but ab initio predictions of RNA interactions are not possible without prev […]

library_books

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

2016
Bioinformatics
PMCID: 4894278
PMID: 26787667
DOI: 10.1093/bioinformatics/btw003

[…] nces in ranks of classifiers over multiple datasets, confirming the feasibility of orthogonality as a way to induce discriminative and parsimonious factor models. We compared iONMF with GraphProt and RNAContext on the same dataset used by Maticzka et al. (). iONMF performed best on 13 out of 24 RBP experiments (AUC=0.907±0.041). Critical difference diagrams show equivalent performance of iONMF and […]

library_books

Revealing protein–lncRNA interaction

2015
Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] straints in the context of motif discovery at RBP binding sites can be found in []. The already mentioned MEMERIS [], CMfinder [], RNApromo [], StructRED [], the algorithm by Li and collaborators [], RNAcontext and RBPmotif [, ], GraphProt [] and Zagros [] are all tools that use, with different strategies and to different extent, secondary structure information to determine more specific binding m […]


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RNAcontext institution(s)
Department of Computer Science, University of Toronto, Toronto, ON, Canada

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