ArticleGenome biology2024
EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics.
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 32 papers.
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Who cites it
32 citing papers in PubMed.
- Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation.Animals : an open access journal from MDPI · 2026Review
- Hybrid CNN and multi-head attention model for analyzing epigenetic mechanisms and gene expression across fungal phylogenetic distances.iScience · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- [Applications and Challenges of Deep Learning in Human Genome Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026Review
- Context-aware sequence-to-function model of human gene regulation.Nature communications · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
- Interpretable fine-tuned large language models facilitate making genetic test decisions for rare diseases.NPJ digital medicine · 2026Article
- Deep learning and attention mechanisms to identify key genes and their implications for the origin of insect wings.Scientific reports · 2026Article
- Transformers for single-cell RNA sequencing: a survey.Briefings in bioinformatics · 2026Review
- A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.Nature communications · 2026Article
- Beyond the baseline: mapping the context-specific regulatory landscape of disease.Trends in genetics : TIG · 2026Review
- EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.Nature communications · 2026Article
- Artificial intelligence models: transforming early diagnosis and precise treatment of gastrointestinal cancers.Molecular cancer · 2026Review
- Large language models for bioinformatics.Quantitative biology (Beijing, China) · 2026Review
- CMC-WDTK: CpG methylation change prediction by a weight-sharing dual-branch Transformer-Kolmogorov-Arnold network model.BMC genomics · 2026Article
- Harnessing artificial intelligence for genomic variant prediction: advances, challenges, and future directions.GigaScience · 2026Review
- Cross-species prediction of histone modifications in plants via deep learning.Genome biology · 2026Article
- A comprehensive survey of genome language models in bioinformatics.Briefings in bioinformatics · 2026Review
- Research Hotspots and Emerging Trends in Osteoporosis Epigenetics.Genetics research · 2026Article
- Deep learning for regulatory genomics: a survey of models, challenges, and applications.Bioinformatics advances · 2026Review
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5 authors.
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Abstract
The inherent similarities between natural language and biological sequences have inspired the use of large language models in genomics, but current models struggle to incorporate chromatin interactions or predict in unseen cellular contexts. To address this, we propose EpiGePT, a transformer-based model designed for predicting context-specific human epigenomic signals. By incorporating transcription factor activities and 3D genome interactions, EpiGePT outperforms existing methods in epigenomic signal prediction tasks, especially in cell-type-specific long-range interaction predictions and genetic variant impacts, advancing our understanding of gene regulation. A free online prediction service is available at http://health.tsinghua.edu.cn/epigept .
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