ArticleGenome biology2018
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- An encyclopedic regulatory and functional atlas of RNA interactomes.Nature methods · 2026Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- PCLIPtools: a robust framework for identifying RNA-protein interaction sites from PAR-CLIP experiments.Nucleic acids research · 2026Article
- PCLIPtools: A Robust Framework for Identifying RNA-Protein Interaction Sites from PAR-CLIP experiments.bioRxiv : the preprint server for biology · 2025Article
- PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking.eLife · 2024Article
- PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking.bioRxiv : the preprint server for biology · 2024Article
- Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.STAR protocols · 2024Article
- MNature communications · 2024Article
- An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains.Molecular cell · 2024Article
- A lncRNA from the FTO locus acts as a suppressor of the mMolecular cell · 2023Article
- Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.Cell genomics · 2023Article
- Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs.Nucleic acids research · 2023Article
- Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.Genome biology · 2023Article
- Analyzing RNA-Protein Interactions by Cross-Link Rates and CLIP-seq Libraries.Current protocols · 2023Article
- Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.Genome biology · 2022Article
- Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell reports methods · 2021Article
- Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing.Frontiers in genetics · 2021Article
- Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.GigaScience · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein - RNA interaction sites. However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. omniCLIP jointly models data across replicates and can integrate background information. Therefore, omniCLIP greatly simplifies the data analysis, increases the reliability of results and paves the way for integrative studies based on data from different assays.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.