ArticleNucleic acids research2019
beRBP: binding estimation for human RNA-binding proteins.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 47 citations in OpenAlex.
- Accessibility in proteins and RNAs interactions prediction with machine learning: are we overlooking non-experts?Briefings in bioinformatics · 2026Review
- LncRNA CASC19 promotes pancreatic cancer progression by increasing PSPC1 protein stability and facilitating the oncogenic PSPC1/ β-Catenin pathway.Molecular medicine (Cambridge, Mass.) · 2025Article
- TTK promotes mitophagy by regulating ULK1 phosphorylation and pre-mRNA splicing to inhibit mitochondrial apoptosis in bladder cancer.Cell death and differentiation · 2025Article
- RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.BMC biology · 2025Article
- Circular RNA Identification and Characterization with CircRNAFlow: A Bioinformatics Approach.Advances in experimental medicine and biology · 2025Article
- DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity.BMC bioinformatics · 2024Article
- RNA-protein interaction prediction without high-throughput data: An overview and benchmark ofComputational and structural biotechnology journal · 2024Article
- EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles.Journal of molecular biology · 2024Article
- C2CDB: an advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs.Bioinformatics advances · 2024Article
- Article
- 3'untranslated regions of tumor suppressor genes evolved specific features to favor cancer resistance.Oncogene · 2022Article
- CRAFT: a bioinformatics software for custom prediction of circular RNA functions.Briefings in bioinformatics · 2022Article
- Prediction of RNA-protein interactions using a nucleotide language model.Bioinformatics advances · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.PLoS computational biology · 2022Article
- RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery.iScience · 2021Article
- Decoding disease: from genomes to networks to phenotypes.Nature reviews. Genetics · 2021Review
- MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Bioinformatic Analysis of Circular RNA Expression.Methods in molecular biology (Clifton, N.J.) · 2021Article
- RBPsuite: RNA-protein binding sites prediction suite based on deep learning.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Identifying binding targets of RNA-binding proteins (RBPs) can greatly facilitate our understanding of their functional mechanisms. Most computational methods employ machine learning to train classifiers on either RBP-specific targets or pooled RBP-RNA interactions. The former strategy is more powerful, but it only applies to a few RBPs with a large number of known targets; conversely, the latter strategy sacrifices prediction accuracy for a wider application, since specific interaction features are inevitably obscured through pooling heterogeneous datasets. Here, we present beRBP, a dual approach to predict human RBP-RNA interaction given PWM of a RBP and one RNA sequence. Based on Random Forests, beRBP not only builds a specific model for each RBP with a decent number of known targets, but also develops a general model for RBPs with limited or null known targets. The specific and general models both compared well with existing methods on three benchmark datasets. Notably, the general model achieved a better performance than existing methods on most novel RBPs. Overall, as a composite solution overarching the RBP-specific and RBP-General strategies, beRBP is a promising tool for human RBP binding estimation with good prediction accuracy and a broad application scope.
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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.