ArticleGenome biology2013
PARma: identification of microRNA target sites in AGO-PAR-CLIP data.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.RNA biology · 2025Article
- MiRNA fine tuning for crop improvement: using advance computational models and biotechnological tools.Molecular biology reports · 2022Review
- Noncoding RNAs in B cell responses.RNA biology · 2021Review
- Argonaute binding within 3'-untranslated regions poorly predicts gene repression.Nucleic acids research · 2020Article
- Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins.Quantitative biology (Beijing, China) · 2020Article
- Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery.PLoS pathogens · 2019Article
- PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks.PLoS computational biology · 2019Article
- Global identification of functional microRNA-mRNA interactions in Drosophila.Nature communications · 2019Article
- Recent computational developments on CLIP-seq data analysis and microRNA targeting implications.Briefings in bioinformatics · 2018Review
- microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions.Nature communications · 2018Article
- A systematic approach to RNA-associated motif discovery.BMC genomics · 2018Article
- Bioinformatic tools for analysis of CLIP ribonucleoprotein data.Wiley interdisciplinary reviews. RNA · 2017Review
- From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.Nucleic acids research · 2017Article
- Epstein-Barr viral miRNAs inhibit antiviral CD4+ T cell responses targeting IL-12 and peptide processing.The Journal of experimental medicine · 2016Article
- Article
- Dynamic miRNA-mRNA paradigms: New faces of miRNAs.Biochemistry and biophysics reports · 2015Review
- Count ratio model reveals bias affecting NGS fold changes.Nucleic acids research · 2015Article
- miRNA-26b Overexpression in Ulcerative Colitis-associated Carcinogenesis.Inflammatory bowel diseases · 2015Article
- Design and bioinformatics analysis of genome-wide CLIP experiments.Nucleic acids research · 2015Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma.
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Registered trials
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