ArticleBioinformatics (Oxford, England)2017
omiXcore: a web server for prediction of protein interactions with large RNA.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Regulation of partial endothelial-to-mesenchymal transition by circATXN1 in ischemic diseases.Nature communications · 2025Article
- Emerging RNA-centric technologies to probe RNA-protein interactions: importance in decoding the life cycle of positive sense single strand RNA viruses and antiviral discovery.Frontiers in cellular and infection microbiology · 2025Review
- Exploring the landscape of tools and resources for the analysis of long non-coding RNAs.Computational and structural biotechnology journal · 2023Review
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- RBPsuite: RNA-protein binding sites prediction suite based on deep learning.BMC genomics · 2020Article
- Structural analysis of SARS-CoV-2 genome and predictions of the human interactome.Nucleic acids research · 2020Article
- Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners.Biochemical Society transactions · 2020Review
- Genistein Represses HOTAIR/Chromatin Remodeling Pathways to Suppress Kidney Cancer.Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology · 2020Article
- RNA structure drives interaction with proteins.Nature communications · 2019Article
- The moonlighting RNA-binding activity of cytosolic serine hydroxymethyltransferase contributes to control compartmentalization of serine metabolism.Nucleic acids research · 2019Article
- An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome.Cell reports · 2018Article
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Authors and funding
3 authors.
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Abstract
summaryHere we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding sites.
resultsomiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to prioritize candidates for further experimental validation. AVAILABILITY AND IMPLEMENTATION: omiXcore is freely accessed on the web at http://service.tartaglialab.com/grant_submission/omixcore. CONTACT: gian.tartaglia@crg.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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