ArticleNucleic acids research2017
Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing.Genome research · 2025Pooled it
- Tools and tactics for studying alternative splicing.Nature reviews. Genetics · 2026Review
- RNA-binding proteins connect Exon usage to the chromatin.NAR genomics and bioinformatics · 2025Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization.PLoS computational biology · 2024Article
- Advances in alternative splicing identification: deep learning and pantranscriptome.Frontiers in plant science · 2023Article
- BARD1 mystery: tumor suppressors are cancer susceptibility genes.BMC cancer · 2022Review
- Article
- Regulatory roles and mechanisms of alternative RNA splicing in adipogenesis and human metabolic health.Cell & bioscience · 2021Review
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework.Frontiers in cell and developmental biology · 2021Article
- Computational Prediction of Protein Arginine Methylation Based on Composition-Transition-Distribution Features.ACS omega · 2020Article
- Uncovering the key dimensions of high-throughput biomolecular data using deep learning.Nucleic acids research · 2020Article
- Specific histone modifications associate with alternative exon selection during mammalian development.Nucleic acids research · 2020Article
- Article
- Identifying Antioxidant Proteins by Using Amino Acid Composition and Protein-Protein Interactions.Frontiers in cell and developmental biology · 2020Article
- A Method for Identifying Vesicle Transport Proteins Based on LibSVM and MRMD.Computational and mathematical methods in medicine · 2020Article
- Identification and Classification of Enhancers Using Dimension Reduction Technique and Recurrent Neural Network.Computational and mathematical methods in medicine · 2020Article
- Discrimination of Thermophilic Proteins and Non-thermophilic Proteins Using Feature Dimension Reduction.Frontiers in bioengineering and biotechnology · 2020Article
- PredAmyl-MLP: Prediction of Amyloid Proteins Using Multilayer Perceptron.Computational and mathematical methods in medicine · 2020Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network. With the advantages of epigenetic features, DeepCode significantly improves the performance in predicting the splicing patterns and their changes during hESC differentiation. Meanwhile, DeepCode reveals the superiority of epigenomic features and their dominant roles in decoding AS patterns, highlighting the necessity of including the epigenetic properties when assembling a more comprehensive splicing code. Moreover, DeepCode allows the robust predictions across cell lineages and datasets. Especially, we identified a putative H3K36me3-regulated AS event leading to a nonsense-mediated mRNA decay of BARD1. Reduced BARD1 expression results in the attenuation of ATM/ATR signalling activities and further the hESC differentiation. These results suggest a novel candidate mechanism linking histone modifications to hESC fate decision. In addition, when trained in different contexts, DeepCode can be expanded to a variety of biological and biomedical fields.
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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.