ArticleGenome biology2024
Splam: a deep-learning-based splice site predictor that improves spliced alignments.
Article in Genome biology, 2024. 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.
- Review
- Predicting human mRNA isoform levels from site-specific splicing kineticsbioRxiv : the preprint server for biology · 2026Article
- Application of deep learning in crop research: From genomics to phenomics.The plant genome · 2026Review
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Spliceread: improving canonical and non-canonical splice site prediction with residual blocks and synthetic data augmentation.BMC bioinformatics · 2026Article
- DeepSAP: improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring.Genome biology · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.Genome biology · 2026Article
- SpliceRead: Improving Canonical and Non-Canonical Splice Site Prediction with Residual Blocks and Synthetic Data Augmentation.bioRxiv : the preprint server for biology · 2026Article
- Utilisation of Machine Learning Approaches Improves RNA-Seq Transcriptome Analyses in Alzheimer's Disease Brain.Journal of molecular neuroscience : MN · 2026Article
- Improving spliced alignment by modeling splice sites with deep learning.Algorithms for molecular biology : AMB · 2026Article
- Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data.Nature communications · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- A basic framework to explain splice-site choice in eukaryotes.Nature communications · 2025Article
- mRNA Isoforms and Variants in Health and Disease.International journal of molecular sciences · 2025Review
- Article
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- Discovering Intron Gain Events in Humans Through Large-Scale Evolutionary Comparisons.Genome biology and evolution · 2025Article
- Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions.Current opinion in structural biology · 2025Review
- Upstream open reading frames may contain hundreds of novel human exons.PLoS computational biology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. We describe Splam, a novel method for predicting splice junctions in DNA using deep residual convolutional neural networks. Unlike previous models, Splam looks at a 400-base-pair window flanking each splice site, reflecting the biological splicing process that relies primarily on signals within this window. Splam also trains on donor and acceptor pairs together, mirroring how the splicing machinery recognizes both ends of each intron. Compared to SpliceAI, Splam is consistently more accurate, achieving 96% accuracy in predicting human splice junctions.
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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.