ArticleNature biotechnology2022
DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it, 120 citations in OpenAlex.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
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- Multi-Tissue Crosstalk Regulating Meniscus Healing Under Inflammation and Physiological Loading.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- Tissue and cellular spatiotemporal dynamics in colon aging.Nature biotechnology · 2026Article
- Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.Molecular systems biology · 2026Article
- A transcriptional patient map of systemic lupus erythematosus reveals disease-related multicellular immune programs conserved between blood and kidney.bioRxiv : the preprint server for biology · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro.bioRxiv : the preprint server for biology · 2026Article
- Tracing cell communication programs across conditions at single cell resolution with CCC-RISE.bioRxiv : the preprint server for biology · 2026Article
- High-content CRISPR activation screens identify synthetically lethal RNA-based mechanisms to sensitize cancer cells to targeted T cell cytotoxicity.Nature genetics · 2026Article
- Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling.Nature communications · 2026Article
- Spatial profiling uncovers multicellular dynamics in early relapse of hepatitis B virus-associated follicular lymphoma.Communications biology · 2026Article
- Impact and correction of segmentation errors in spatial transcriptomics.Nature genetics · 2026Article
- Pertpy: an end-to-end framework for perturbation analysis.Nature methods · 2026Article
- Temporal tissue dynamics from a spatial snapshot.Nature · 2026Article
- DisCP-Atlas: a comprehensive resource mapping cellular processes to complex diseases.Nucleic acids research · 2026Article
- Integrative multi-omics dissection identifies ACO2, KLF5, and IMP4 as central regulators of the mitochondrial-immune axis in ulcerative colitis.Frontiers in immunology · 2026Article
- Multi-functional Small Molecule for Regenerative Healing of Avascular Meniscus Tears: Modulation of Inflammation, Differentiation, and Multi-Tissue Crosstalk.Theranostics · 2026Article
14 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
Funding
Abstract
Deciphering the functional interactions of cells in tissues remains a major challenge. Here we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs)-combinations of coordinated cellular programs in different cell types that form higher-order functional units at the tissue level-from either spatial data or single-cell data obtained without spatial information. Tested on spatial datasets from the mouse hypothalamus, cerebellum, visual cortex and neocortex, DIALOGUE identified MCPs associated with animal behavior and recovered spatial properties when tested on unseen data while outperforming other methods and metrics. In spatial data from human lung cancer, DIALOGUE identified MCPs marking immune activation and tissue remodeling. Applied to single-cell RNA sequencing data across individuals or regions, DIALOGUE uncovered MCPs marking Alzheimer's disease, ulcerative colitis and resistance to cancer immunotherapy. These programs were predictive of disease outcome and predisposition in independent cohorts and included risk genes from genome-wide association studies. DIALOGUE enables the analysis of multicellular regulation in health and disease.
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