ArticleScience advances2025
ChromoGen: Diffusion model predicts single-cell chromatin conformations.
Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles.Nucleic acids research · 2026Article
- Review
- 3D chromatin structure remodelling in cancer.Cell communication and signaling : CCS · 2026Review
- Epigenetic remodeling during UV exposure: high resolution analysis of histone post-translational modifications in a DNA binding protein 2 mutant model.Histochemistry and cell biology · 2026Article
- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- Large-scale data-driven pre-trained DNA models enhance performance across diverse genomics tasks.Nature communications · 2026Article
- PVAED: prior-guided variational autoencoders with diffusion denoising for interpretable single-cell representation learning.Briefings in bioinformatics · 2026Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.Bioinformatics (Oxford, England) · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.ArXiv · 2025Article
- 3D Genome Architecture in Stem Cell Lineage Commitment: from Structural Organization to Precision Regulation.Advanced genetics (Hoboken, N.J.) · 2025Review
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Breakthroughs in high-throughput sequencing and microscopic imaging technologies have revealed that chromatin structures vary considerably between cells of the same type. However, a thorough characterization of this heterogeneity remains elusive due to the labor-intensive and time-consuming nature of these experiments. To address these challenges, we introduce ChromoGen, a generative model based on state-of-the-art artificial intelligence techniques that efficiently predicts three-dimensional, single-cell chromatin conformations de novo with both region and cell type specificity. These generated conformations accurately reproduce experimental results at both the single-cell and population levels. Moreover, ChromoGen successfully transfers to cell types excluded from the training data using just DNA sequence and widely available DNase-seq data, thus providing access to chromatin structures in myriad cell types. These achievements come at a remarkably low computational cost. Therefore, ChromoGen enables the systematic investigation of single-cell chromatin organization, its heterogeneity, and its relationship to sequencing data, all while remaining economical.
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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.