ArticleRNA (New York, N.Y.)2018
A sequence-based, deep learning model accurately predicts RNA splicing branchpoints.
Article in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 81 citations in OpenAlex.
- Protocol for identification of intronic lariat RNAs by RNA deep sequencing in Arabidopsis thaliana.STAR protocols · 2026Article
- Blood-based RNA-Seq of 5412 individuals with rare disease identifies new candidate diagnoses in the National Genomic Research Library.medRxiv : the preprint server for health sciences · 2026Article
- The human branchpoint-interacting stem-loop sequence and structure regulates U2 snRNA expression, branchpoint recognition, and the transcriptome.Nucleic acids research · 2026Article
- RNA localization to nuclear speckles follows splicing logic.Nucleic acids research · 2026Article
- Genome-wide functional annotation and interpretation of splicing variants: toward RNA-targeted therapies.Journal of human genetics · 2025Review
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- A validated heart-specific model for splice-disrupting variants in childhood heart disease.Genome medicine · 2024Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons.Nucleic acids research · 2024Article
- Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction.Briefings in bioinformatics · 2024Article
- Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases.Frontiers in bioscience (Scholar edition) · 2024Review
- Practical Recommendations for the Selection of Patients for Individualized Splice-Switching ASO-Based Treatments.Human mutation · 2024Review
- Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species.Nucleic acids research · 2023Article
- Use of genome sequencing to hunt for cryptic second-hit variants: analysis of 31 cases recruited to the 100 000 Genomes Project.Journal of medical genetics · 2023Article
- Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts.Nature structural & molecular biology · 2023Article
- Article
- Harnessing the potential of machine learning and artificial intelligence for dementia research.Brain informatics · 2023Review
- A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing.EMBO molecular medicine · 2023Article
- The role of noncoding genetic variants in cardiomyopathy.Frontiers in cardiovascular medicine · 2023Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Experimental detection of RNA splicing branchpoints is difficult. To date, high-confidence experimental annotations exist for 18% of 3' splice sites in the human genome. We develop a deep-learning-based branchpoint predictor, LaBranchoR, which predicts a correct branchpoint for at least 75% of 3' splice sites genome-wide. Detailed analysis of cases in which our predicted branchpoint deviates from experimental data suggests a correct branchpoint is predicted in over 90% of cases. We use our predicted branchpoints to identify a novel sequence element upstream of branchpoints consistent with extended U2 snRNA base-pairing, show an association between weak branchpoints and alternative splicing, and explore the effects of genetic variants on branchpoints. We provide genome-wide branchpoint annotations and in silico mutagenesis scores at http://bejerano.stanford.edu/labranchor.
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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.