A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.

By K. Miranda, Tien Huynh, Yvonne Tay, Yen-Sin Ang, W. Tam, A. Thomson, Bing Lim, Isidore Rigoutsos. Cell, 2006

2,076 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/82299d17c9fb3b83dc1351238b87d83a7f4d1e57

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Citations in the corpus

MicroRNAs and complex diseases: from experimental results to computational models (2019, positive): “proposed a patternbased method for the identification of miRNA binding sites and their corresponding heteroduplexes [86].”
The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2 (2011, background): “dtd" [ ]> MicroRNAs (miRNAs) are endogenous noncoding RNAs, about 22 nucleotides in length, that mediate post-transcriptional gene silencing by annealing to inexactly complementary sequences in the 3′-untranslated regions of target mRNA”
Revisiting the principles of microRNA target recognition and mode of action (2009, methodology): “Although bioinformatics search tools were used to identify precise sites in these message”
MicroRNA targeting specificity in mammals: determinants beyond seed pairing. (2007, result): “We also examined the results of a different approach that predicted sites with extensive WatsonCrick and G:U pairing along the length of the miRNA and tolerated imperfect seed matches (Miranda et al., 2006).”
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype (2007, background): “In humans, at least 10% of the protein-coding mRNAs might be conserved targets of miRNAs [38,39,41-49].”
Supplemental Information Supplemental Data (2014, neutral): “…databases were used: MIRDB release 14 (Wang, 2008; Wang and El Naqa, 2008), Targetscan 5.1 (Friedman et al, 2009), MICROCOSM v5 (Griffiths-Jones et al, 2008), DIANA 3.0 (Maragkakis et al, 2009a; Maragkakis et al, 2009b), RNA22 (august 2007) (Miranda et al, 2006) and PITA v6 (Kertesz et al, 2007).”
miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets (2012, methodology): “Moreover, rna22 identifies putative miRNAs by mapping their binding sites through a pattern-based approach [17], and PITA incorporates free energy intake and cost to evaluate the interactions between miRNAs and gene targets [18].”
miRecords: an integrated resource for microRNA–target interactions (2008, background): “Comparative studies conducted with the earlier miRNA target prediction programs (including TargetScanS, PicTar, miRanda, DIANA-microT, RNAhybrid, MicroInspector and Rna22) suggested that no one program was consistently superior to all others (13,29).”
miR-19 is a key oncogenic component of mir-17-92. (2009, positive): “4A; Miranda et al. 2006).”
Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver. (2012, positive): “The RNA22 algorithm (31) identified a potential miR-122 binding site in the 3 ′ UTR of Ccl2 (Figure 4K).”
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data (2013, methodology): “Genomic coordinates of these conserved miRNAs target sites predicted by TargetScan (25), miRanda/mirSVR (27), PITA (28), Pictar 2.0 (19) and RNA22 (29) were collected and converted to hg19, mm9/ mm10 and ce6/ce10 assemblies using LiftOver, respectively.”
MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene (2008, methodology): “PDCD4 30-UTR contains an MRE for miR-21 Four different computational methods were employed to identify over 100 genes that are predicted to be targets of miR-21 by at least two out of four methods: Miranda, TargetScan, rna22 and PicTar (John et al., 2004; Krek et al., 2005; Lewis et al., 2005; Miran”