ArticleNature methods2022
MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Integrating single-cell RNA sequencing with multi-omics to decode disease microenvironments.Molecular biology reports · 2026Review
- Sequential and coordinated control of human plasma cell differentiation by IRF4 and BLIMP1 utilizing a discriminating ISRE/EICE motif lexicon.bioRxiv : the preprint server for biology · 2026Article
- BLIMP1 shapes germinal center B cell clonal diversity by gating chromatin accessibility during light-to-dark zone transition.Nature immunology · 2026Article
- Corneal Innervation Research at a Crossroads: A Tool-Driven Roadmap for the Future.Investigative ophthalmology & visual science · 2026Review
- Interpretable modality-aware mapping of gene regulation in single-cell multiomics with scMAGCA.Nature communications · 2026Article
- A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation.Nature communications · 2026Article
- Temporal AI model predicts drivers of cell state trajectories across human aging.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking LLM-based agents for single-cell omics analysis.Genome biology · 2026Article
- IFNγ-induced IRF1 synergizes with TLR7 signals to tune the IRF4-IRF8 axis and drive pathogenic effector B cell fate.bioRxiv : the preprint server for biology · 2026Article
- Multi-view deep learning of highly multiplexed imaging data improves association of cell states with clinical outcomes.Bioinformatics advances · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- Gene regulatory network inference with popInfer reveals the dynamic regulation of hematopoietic stem cell quiescence.iScience · 2025Article
- MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis.Genes & development · 2025Article
- Single-cell multiomics data integration and generation with scPairing.Cell reports methods · 2025Article
- PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories.Nature methods · 2025Article
- Multitask benchmarking of single-cell multimodal omics integration methods.Nature methods · 2025Article
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6 authors.
Funding
Abstract
Rigorously comparing gene expression and chromatin accessibility in the same single cells could illuminate the logic of how coupling or decoupling of these mechanisms regulates fate commitment. Here we present MIRA, probabilistic multimodal models for integrated regulatory analysis, a comprehensive methodology that systematically contrasts transcription and accessibility to infer the regulatory circuitry driving cells along cell state trajectories. MIRA leverages topic modeling of cell states and regulatory potential modeling of individual gene loci. MIRA thereby represents cell states in an efficient and interpretable latent space, infers high-fidelity cell state trees, determines key regulators of fate decisions at branch points and exposes the variable influence of local accessibility on transcription at distinct loci. Applied to epidermal differentiation and embryonic brain development from two different multimodal platforms, MIRA revealed that early developmental genes were tightly regulated by local chromatin landscape whereas terminal fate genes were titrated without requiring extensive chromatin remodeling.
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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.