ArticleMolecular cell2023
HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.
Article in Molecular cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Mammalian therapeutic riboswitches: Engineering and custom ligands.Molecular therapy. Nucleic acids · 2026Review
- ARID5A RNA-binding coordinates microglial defense and ferroptosis in iPSC-derived models.Nature communications · 2026Article
- RIBEX: predicting and explaining RNA binding across structured and intrinsically disordered regions (IDR)-rich proteins.Bioinformatics (Oxford, England) · 2026Article
- The HIV-1 restriction factor RPRD2 does not inhibit transcription of HIV-1 or endogenous retroelements.bioRxiv : the preprint server for biology · 2026Article
- K-attention: a biologically informed attention operator for data-efficient sequence-based omics modeling.Briefings in bioinformatics · 2026Article
- The Use of Deep Learning in RNA Therapeutic Development.ACS nano · 2026Review
- RNA-binding protein transcripts reflect composition of target mRNAs.Nucleic acids research · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- A framework for the exploration of subcellular compartmentalization of RNA-binding proteins.Nature communications · 2026Article
- Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.Cancer research · 2026Article
- RNA-coupled CRISPR screens reveal ZNF207 as a regulator of LMNA aberrant splicing in progeria.Molecular cell · 2026Article
- Interpretable prediction of nucleic acid-binding proteins using a protein language model.Bioinformatics advances · 2026Article
- Key RNA-binding proteins in renal fibrosis: a comprehensive bioinformatics and machine learning framework for diagnostic and therapeutic insights.Renal failure · 2025Article
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- FASTK post-transcriptional regulators - a 'FAST-tracK' in mitochondrial gene expression.Biochemical Society transactions · 2025Review
- The molecular chaperone TRAP1 promotes translation ofRNA (New York, N.Y.) · 2025Article
- RNA triggers chronic stress during neuronal aging.bioRxiv : the preprint server for biology · 2025Article
- RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.Nucleic acids research · 2025Article
- Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress.Nature neuroscience · 2025Article
- An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions.Nature communications · 2025Article
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13 authors.
Funding
Abstract
RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier (HydRA), which leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. Occlusion mapping by HydRA robustly detects known RBDs and predicts hundreds of uncharacterized RNA-binding associated domains. Enhanced CLIP (eCLIP) for HydRA-predicted RBP candidates reveals transcriptome-wide RNA targets and confirms RNA-binding activity for HydRA-predicted RNA-binding associated domains. HydRA accelerates construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.
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