ArticleNature methods2026
Decoding sequence determinants of gene expression in diverse cellular and disease states.
Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles.Nucleic acids research · 2026Article
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- GUANinE v1.1 reveals complementarity of supervised and genomic language models.Bioinformatics (Oxford, England) · 2026Article
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles.bioRxiv : the preprint server for biology · 2026Article
- Teaching an old dog new cells.Nature methods · 2026Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- Beyond the baseline: mapping the context-specific regulatory landscape of disease.Trends in genetics : TIG · 2026Review
- Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.Genome biology · 2026Article
- Uncertainty-aware genomic deep learning with knowledge distillation.NPJ artificial intelligence · 2026Article
- Article
- gReLU: a comprehensive framework for DNA sequence modeling and design.Nature methods · 2025Article
- UNICORN: Towards universal cellular expression prediction with a multi-task learning framework.Nature communications · 2025Article
- Programming human cell type-specific gene expression via an atlas of AI-designed enhancers.bioRxiv : the preprint server for biology · 2025Article
- Fine-tuning sequence to function deep learning models on large-scale proteomic data improves the accuracy of variant effect prediction.bioRxiv : the preprint server for biology · 2025Article
- Flashzoi: an enhanced Borzoi for accelerated genomic analysis.Bioinformatics (Oxford, England) · 2025Article
- Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies.Integrative and comparative biology · 2025Review
- Polygraph: a software framework for the systematic assessment of synthetic regulatory DNA elements.Genome biology · 2025Article
- Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2.PLoS computational biology · 2025Article
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence-to-function models that predict gene expression from genomic DNA sequence have proven valuable for many biological tasks, including understanding cis-regulatory syntax and interpreting noncoding genetic variation. However, current state-of-the-art models are trained largely on bulk expression profiles from healthy tissues or cell lines and have not learned the properties of precise cell types and states that are captured in large-scale single-cell transcriptomic datasets. Thus, they cannot perform these tasks at the resolution of specific cell types or states. Here we present Decima, a model that predicts the cell type- and condition-specific expression of a gene from its surrounding DNA sequence. Decima is trained on single-cell or single-nucleus RNA sequencing data from over 22 million cells and successfully predicts the cell-type-specific expression of unseen genes. We demonstrate Decima's ability to reveal cis-regulatory mechanisms driving cell-type-specific gene expression and its changes in disease, predict noncoding-variant effects at cell type resolution and design context-specific regulatory DNA elements.
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