ArticleMethods in molecular biology (Clifton, N.J.)2022
RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment.
Article in Methods in molecular biology (Clifton, N.J.), 2022. 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.
- RBP-Driven RNA sorting and local translation establish the molecular identities of individual sensory axons.Nature communications · 2026Article
- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- Human-specific sequence features in HTT exon 1 promote toxic misprocessing via splicing factor SRSF7.Nature communications · 2026Article
- NAT10-mediated N4-acetylcytidine modification drives RNA splicing of PML to alleviate adipose-derived stem cell senescence and promote diabetic wound healing.Clinical and translational medicine · 2026Article
- CircNSD2 promotes metastasis and immune escape by increasing the USP10/SRSF6-mediated alternative splicing of TPM1 in TNBC.Molecular cancer · 2026Article
- CYFIP1 governs the development of cortical axons by modulating calcium availability.Nature communications · 2025Article
- Widespread prevalence of CD19 exon 5-6 skipping in primary pediatric B-Cell acute lymphoblastic leukemia patients.Molecular and cellular pediatrics · 2025Article
- Dysregulated RNA-binding proteins and alternative splicing: Emerging roles in autism spectrum disorder.Molecules and cells · 2025Review
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- p53 activates circASCC3 to repress R-loops and enhance resistance to chemotherapy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- LncRNA ENST00000581911 Regulates Extraocular Muscle Remodeling by Interacting With KHSRP in Thyroid Eye Disease.Investigative ophthalmology & visual science · 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
- Demonstration of the pathogenicity of a common non-exomic mutation in ABCA4 using iPSC-derived retinal organoids and retrospective clinical data.Human molecular genetics · 2024Article
- Transcriptomic analysis reveals regulation of adipogenesis via long non-coding RNA, alternative splicing, and alternative polyadenylation.Scientific reports · 2024Article
- Mechanistic insights into the basis of widespread RNA localization.Nature cell biology · 2024Review
- Article
- Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers.Biomedicines · 2024Review
- CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing.The EMBO journal · 2023Article
- Long non-coding RNA generated from CDKN1A gene by alternative polyadenylation regulates p21 expression during DNA damage response.Nucleic acids research · 2023Article
- Long-read sequencing reveals the landscape of aberrant alternative splicing and novel therapeutic target in colorectal cancer.Genome medicine · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-binding proteins (RBPs) play a key role in post-transcriptional regulation via binding to coding and non-coding RNAs. Recent development in experimental technologies, aimed to identify the targets of RBPs, has significantly broadened our knowledge on protein-RNA interactions. However, for many RBPs in many organisms and cell types, experimental RNA-binding data is not available. In this chapter we describe a computational approach, named RBPmap, available as a web service via http://rbpmap.technion.ac.il/ and as a stand-alone version for download. RBPmap was designed for mapping and predicting the binding sites of any RBP within a nucleic acid sequence, given the availability of an experimentally defined binding motif of the RBP. The algorithm searches for a sub-sequence that significantly matches the RBP motif, considering the clustering propensity of other weak matches within the motif environment. Here, we present different applications of RBPmap for discovering the involvement of RBPs and their targets in a variety of cellular processes, in health and disease states. Finally, we demonstrate the performance of RBPmap in predicting the binding targets of RBPs in large-scale RNA-binding data, reinforcing the strength of the tool in distinguishing cognate binding sites from weak motifs.
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Registered trials
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