ArticleNature methods2025
scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution.
Article in Nature methods, 2025. 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.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- ATACompass enables cross-species cell identity mapping for scATAC-seq without gene annotations.Cell reports methods · 2026Article
- Context-aware sequence-to-function model of human gene regulation.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
- Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.Bioinformatics (Oxford, England) · 2026Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- ModelingbioRxiv : the preprint server for biology · 2026Article
- Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.Genome biology · 2026Article
- Medea: An omics AI agent for therapeutic discovery.bioRxiv : the preprint server for biology · 2026Article
- Article
- Uncertainty-aware genomic deep learning with knowledge distillation.NPJ artificial intelligence · 2026Article
- scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution.Nature methods · 2025Article
- Transformative advances in single-cell omics: a comprehensive review of foundation models, multimodal integration and computational ecosystems.Journal of translational medicine · 2025Review
- Programming human cell type-specific gene expression via an atlas of AI-designed enhancers.bioRxiv : the preprint server for biology · 2025Article
- Flashzoi: an enhanced Borzoi for accelerated genomic analysis.Bioinformatics (Oxford, England) · 2025Article
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive molecular impact mapping of common and rare variants at GWAS loci.bioRxiv : the preprint server for biology · 2025Article
- Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
Understanding how regulatory sequences shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA sequencing and epigenomic profiling provides opportunities to build models capturing sequence determinants across steps of gene expression. However, current models, developed primarily for bulk omics data, fail to capture the cellular heterogeneity and dynamic processes revealed by single-cell multimodal technologies. Here, we introduce scooby, a framework to model genomic profiles of single-cell RNA-sequencing coverage and single-cell assay for transposase-accessible chromatin using sequencing insertions from sequence at single-cell resolution. For this, we leverage the pretrained multiomics profile predictor Borzoi and equip it with a cell-specific decoder. Scooby recapitulates cell-specific expression levels of held-out genes and identifies regulators and their putative target genes. Moreover, scooby allows resolving single-cell effects of bulk expression quantitative trait loci and delineating their impact on chromatin accessibility and gene expression. We anticipate scooby to aid unraveling the complexities of gene regulation at the resolution of individual cells.
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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.