Fast and effective prediction of microRNA/target duplexes.

By Marc Rehmsmeier, Peter Steffen, Matthias Hochsmann, Robert Giegerich. RNA: A publication of the RNA Society, 2004

2,511 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/8c1f06689340bbbd5f56d90511a338ebc958c517

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Citations in the corpus

microRNA target predictions in animals (2006, methodology): “None of the other current algorithms (including the latest miRanda predictions, RNAhybri”
miRU: an automated plant miRNA target prediction server (2005, background): “While miRNA‐target duplex free energy may be important for animal miRNA target prediction (7, 8 ), plant miRNA targets can be predicted by sequence similarity since plant miRNA seems to bind almost perfectly to its cognate mRNA (7,9).”
Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. (2005, positive): “end starting at nt 10 with RNAhybrid ( Rehmsmeier et al., 2004 ) and used the worse score.”
RNAplex: a fast tool for RNA-RNA interaction search (2008, methodology): “This idea was first introduced by RNAhybrid (Rehmsmeier et al., 2004) and is also implemented by RNAduplex from the Vienna RNA package.”
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. (2006, methodology): “…for estimating the rate of spurious matches when binding sites are iden-tiﬁed by analyzing the structure and Gibbs energy of a putative complex (Rehmsmeier et al., 2004): indeed, the higher the sequence similarity between m and the putative binding site the better the predicted structure’s…”
Human MicroRNA Targets (2004, background): “Recently, several computational methods for the prediction of miRNA targets have been developed (Enright et al. 2003; Lewis et al. 2003; Rajewsky and Socci 2003; Stark et al. 2003; Kiriakidou et al. 2004; Rehmsmeier et al. 2004).”
ViennaRNA Package 2.0 (2011, result): “RNAduplex , similar to Rehmsmeier ’ s RNAhy-brid [44], ignores intramolecular structures and all multi-branch loops in its search for thermodynamically favorable interaction regions.”
MiRNA-Directed Regulation of VEGF and Other Angiogenic Factors under Hypoxia (2006, methodology): “This was expected, as no binding site for miR-15b or miR-16 was detected by either the miRanda software, RNAhybrid, or FindTar algorithms in the 39-UTR fragment of PTN.”
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions (2008, methodology): “We disregard dangling end energy contributions for the purpose of simplification here and in the following.”
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions (2013, methodology): “Many databases such as microRNA.org (10), miRGen (11), miRGator (12), miRDB (13) and miRNAMap (14) identify miRNA target interactions (MTIs) using a number of target prediction tools like TargetScan (15,16), miRanda (17), PicTar (18), RNAhybrid (19) and PITA (20).”
Bioinformatic discovery of microRNA precursors from human ESTs and introns (2006, methodology): “Optimal free energy and RNA duplex mfe are the output values of RNAhybrid.”