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Common features of microRNA target prediction tools
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Europe PubMed Central
title
Common features of microRNA target prediction tools
(English)
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main subject
microRNA
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based on heuristic
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author name string
Sarah M. Peterson
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1
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Crossref
Jeffrey A. Thompson
series ordinal
2
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Crossref
Melanie L. Ufkin
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3
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Crossref
Pradeep Sathyanarayana
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4
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Lucy Liaw
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5
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Clare Bates Congdon
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6
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language of work or name
English
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PubMed
publication date
2014
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published in
Frontiers in Genetics
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volume
5
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page(s)
23
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PubMed
cites work
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PubMed Central
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Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
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PubMed Central
reference URL
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21 March 2017
miRBase: integrating microRNA annotation and deep-sequencing data
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PubMed Central
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21 March 2017
miRecords: an integrated resource for microRNA-target interactions
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PubMed Central
reference URL
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21 March 2017
Most mammalian mRNAs are conserved targets of microRNAs
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PubMed Central
reference URL
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21 March 2017
miRBase: tools for microRNA genomics
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PubMed Central
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21 March 2017
MicroRNA targeting specificity in mammals: determinants beyond seed pairing
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21 March 2017
Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression
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PubMed Central
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21 March 2017
miTarget: microRNA target gene prediction using a support vector machine
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PubMed Central
reference URL
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21 March 2017
RNAhybrid: microRNA target prediction easy, fast and flexible
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PubMed Central
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21 March 2017
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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21 March 2017
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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21 March 2017
Principles of microRNA-target recognition
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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21 March 2017
Human MicroRNA targets
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PubMed Central
reference URL
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21 March 2017
Fast and effective prediction of microRNA/target duplexes
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
MicroRNA targets in Drosophila
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
Combinatorial microRNA target predictions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
Prediction of mammalian microRNA targets
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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21 March 2017
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
21 March 2017
miRDB: a microRNA target prediction and functional annotation database with a wiki interface
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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21 March 2017
Specificity of microRNA target selection in translational repression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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21 March 2017
The role of site accessibility in microRNA target recognition
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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7 April 2017
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution
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PubMed Central
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7 April 2017
MicroRNAs in Cancer
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PubMed Central
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7 April 2017
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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7 April 2017
miRmap web: Comprehensive microRNA target prediction online
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PubMed Central
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28 September 2017
ComiR: Combinatorial microRNA target prediction tool
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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28 September 2017
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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28 September 2017
The role of microRNAs in cancer susceptibility
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stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Online resources for miRNA analysis.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
One decade of development and evolution of microRNA target prediction algorithms
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Interactive exploration of RNA22 microRNA target predictions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
miR-199b-5p directly targets PODXL and DDR1 and decreased levels of miR-199b-5p correlate with elevated expressions of PODXL and DDR1 in acute myeloid leukemia
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
The role of the precursor structure in the biogenesis of microRNA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
MicroRNAs and developmental timing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
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28 September 2017
Practical Aspects of microRNA Target Prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
MiRonTop: mining microRNAs targets across large scale gene expression studies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Improving performance of mammalian microRNA target prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Survey of Computational Algorithms for MicroRNA Target Prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
mRNA secondary structures fold sequentially but exchange rapidly in vivo
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
miRò: a miRNA knowledge base
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
MicroRNAs: critical mediators of differentiation, development and disease
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
DIANA-microT web server: elucidating microRNA functions through target prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Using expression profiling data to identify human microRNA targets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Structure clustering features on the Sfold Web server
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 September 2017
miRNA-target prediction based on transcriptional regulation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
31 May 2018
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
31 May 2018
Complete suboptimal folding of RNA and the stability of secondary structures.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
31 May 2018
Functional microRNA targets in protein coding sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 November 2018
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 November 2018
HuMiTar: a sequence-based method for prediction of human microRNA targets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 November 2018
Prediction of both conserved and nonconserved microRNA targets in animals.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 November 2018
Naïve Bayes for microRNA target predictions--machine learning for microRNA targets.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 November 2018
Potent effect of target structure on microRNA function.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927079
retrieved
28 November 2018
Identifiers
DOI
10.3389/FGENE.2014.00023
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1038418
OpenCitations bibliographic resource ID
1038418
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1038418
PMCID
3927079
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1038418
PubMed ID
24600468
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
1038418
ResearchGate publication ID
260560570
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