A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
By Shivendra Kishore, Lukasz Jaskiewicz, Lukas Burger, Jean Hausser, Mohsen Khorshid, Mihaela Zavolan. Nature Methods, 2011
468 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/04d103d886af91e28ba10ba3dac5924690cd997c
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In Molecular Biology
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Citations in the corpus
- DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions (2014, result): “Compared to the results obtained by HITS-CLIP, the boundaries of the identified binding locations are sharper and significantly narrower, while T-to-C mutations close to the region occupied by the RNA-induced silencing complex (RISC) contribute to the identification of the exact miRNA recognition el”
- PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data (2011, background): “A recent follow-up study suggested that CCRs could be used for all RBPs [24].”
- Predicting effective microRNA target sites in mammalian mRNAs (2015, methodology): “All mature miRNAs were downloaded from miRBase release 21 ( Kozomara and Griffiths-Jones, 2014 ).”
- Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1 (2017, background): “3A).(1,2,19) Since CLIP data sets do not distinguish HuR”
- m6A-dependent regulation of messenger RNA stability (2013, unknown): “Mild enzyme digestion 33 : The first round of T1 digest was carried out under 0.2 U/µL for 15 min instead of 1 U/µL for 15 min.”
- Expanded identification and characterization of mammalian circular RNAs (2014, background): “Using data from high-throughput in vivo crosslinking experiments, which identified clusters of AGO2crosslinking sites that indicated AGO2 binding [24-26], we compared the density of AGO2-crosslinking clusters within exons that can form circRNAs to the density within their neighboring linear exons.”