ArticleNature methods2024
Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- Inferring cell-specific gene regulatory networks based on causal graph embedding.Cell reports methods · 2026Article
- Spatially resolved transcriptomics identifies intercellular signaling post-ischemic stroke that controls neural stem cell proliferation.Stem cell reports · 2026Article
- iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.Signal transduction and targeted therapy · 2026Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- High altitude-mediated immune remodeling accelerates aging.Science advances · 2026Article
- Spatiotemporal dynamics of mammalian wound healing.Cell discovery · 2026Review
- Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data.NPJ systems biology and applications · 2025Review
- Spatially resolved multi-omics of human metabolic dysfunction-associated steatotic liver disease.Nature genetics · 2025Article
- MAGNET: Multi-view graph autoencoder with cell-gene attention for cell interaction network reconstruction from spatial transcriptomics.PLoS computational biology · 2025Article
- Unpacking PCOS Inflammation: From Misconceptions to Immune Networks.Endocrinology · 2025Review
- Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application.Biomarker research · 2025Review
- Spatial pattern enhanced cellular and tissue recognition for spatial transcriptomics.NAR genomics and bioinformatics · 2025Article
- Quantifying Landscape and Flux from Single-Cell Omics: Unraveling the Physical Mechanisms of Cell Function.JACS Au · 2025Review
- CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics.Nature methods · 2025Article
- RNA-Seq Analysis Revealed the Virulence Regulatory Network Mediated by the Ferric Uptake Regulator (Fur) inMicroorganisms · 2025Article
- Cross-expression meta-analysis of 695 brain samples reveals coordinated gene expression across spatially adjacent cells.bioRxiv : the preprint server for biology · 2025Article
- Spatial Insights in Cardiovascular Aging.Aging and disease · 2025Review
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis.Entropy (Basel, Switzerland) · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
From single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), one can extract high-dimensional gene expression patterns that can be described by intercellular communication networks or decoupled gene modules. These two descriptions of information flow are often assumed to occur independently. However, intercellular communication drives directed flows of information that are mediated by intracellular gene modules, in turn triggering outflows of other signals. Methodologies to describe such intercellular flows are lacking. We present FlowSig, a method that infers communication-driven intercellular flows from scRNA-seq or ST data using graphical causal modeling and conditional independence. We benchmark FlowSig using newly generated experimental cortical organoid data and synthetic data generated from mathematical modeling. We demonstrate FlowSig's utility by applying it to various studies, showing that FlowSig can capture stimulation-induced changes to paracrine signaling in pancreatic islets, demonstrate shifts in intercellular flows due to increasing COVID-19 severity and reconstruct morphogen-driven activator-inhibitor patterns in mouse embryogenesis.
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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 Socratic graph.