ArticleBMC genomics2020
Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 45 citations in OpenAlex.
- An overview of self-supervised deep learning applications to molecular data.Briefings in bioinformatics · 2026Review
- First Exonic Cryptic Branchpoint Variant in an Inherited Retinal Degeneration Detected in an IrishGenes · 2026Article
- A novel phenotype-guided genome analysis pipeline for variant discovery.NPJ genomic medicine · 2026Article
- Cancer genomic profiling predicts pathogenicity ofmedRxiv : the preprint server for health sciences · 2026Article
- Genome-wide functional annotation and interpretation of splicing variants: toward RNA-targeted therapies.Journal of human genetics · 2025Review
- New genetic diagnoses for inherited retinal dystrophies by integrating splicing tools into NGS pipelines.NPJ genomic medicine · 2025Article
- Data-driven insights to inform splice-altering variant assessment.American journal of human genetics · 2025Article
- Refining clinically relevant parameters for mis-splicing risk in shortened introns with donor-to-branchpoint space constraint.European journal of human genetics : EJHG · 2024Article
- SpliceAPP: an interactive web server to predict splicing errors arising from human mutations.BMC genomics · 2024Article
- Exonic splicing code and coordination of divalent metals in proteins.Nucleic acids research · 2024Article
- DeepSplice: a deep learning approach for accurate prediction of alternative splicing events in the human genome.Frontiers in genetics · 2024Article
- 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
- Variations of intronic branchpoint motif: identification and functional implications in splicing and disease.Communications biology · 2023Review
- Evidence-Based Guide to Using Artificial Introns for Tissue-Specific Knockout in Mice.International journal of molecular sciences · 2023Review
- Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans.Genome research · 2023Article
- Article
- Computational prediction of human deep intronic variation.GigaScience · 2022Review
- SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing.Human mutation · 2022Article
- Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing.Nature structural & molecular biology · 2022Article
- Genome-wide detection of human variants that disrupt intronic branchpoints.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
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Authors and funding
32 authors at 8 institutions in 5 countries.
Funding
Abstract
backgroundBranch points (BPs) map within short motifs upstream of acceptor splice sites (3'ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3'ss.
resultsWe used a large set of constitutive and alternative human 3'ss collected from Ensembl (n = 264,787 3'ss) and from in-house RNAseq experiments (n = 51,986 3'ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3'ss (99.48 and 65.84% accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17%.
conclusionsOur investigations revealed that Branchpointer was optimal to detect BPs upstream of 3'ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.
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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.