ArticleGenome research2022
Scalable and model-free detection of spatial patterns and colocalization.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
48 citing papers in PubMed.
- A Hypothalamic Oxytocinergic-Sympathetic Axis Couples Anxiety Dysregulation With Impaired Tendon-Bone Repair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Spatial transcriptomics reveals microenvironmental heterogeneity in osteoarthritic subchondral bone.Nature communications · 2026Article
- Multi-omics characterization of a GPRC5AJournal of translational medicine · 2026Article
- Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies.Cell reports methods · 2026Article
- APOC1⁺IFI30⁺ TAMs orchestrate colorectal cancer liver metastasis by coupling cholesterol biosynthesis with secretion of immunosuppressive factors.Cellular and molecular life sciences : CMLS · 2026Article
- Unraveling cell-cell communication through spatial transcriptomics: a review of computational methods.Briefings in bioinformatics · 2026Review
- Spatial single-cell landscape of tumor-associated macrophages and their crosstalk with the tumor microenvironment.Cell discovery · 2026Article
- BART-spatial unravels biologically significant transcriptional regulators from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- Multi-omic characterization of nasopharyngeal carcinoma delineates the subtype-specific landscape of response to induction chemotherapy.Nature cancer · 2026Article
- Single cell multiomics revealed fibrotic trajectories of endometrial cells and interaction with the pro-fibrotic macrophages in intrauterine adhesion.Genome medicine · 2026Article
- Single-nucleus transcriptomics of an engineered pig model reveals microglia-T cell interactions driving Huntington's disease neurodegeneration.Nature biomedical engineering · 2026Article
- Multi-omics analysis reveals that CAPG positive macrophages are key immunosuppressive drivers and prognostic determinants in the ferroptosis landscape of hepatocellular carcinoma.Discover oncology · 2026Article
- transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- SpaceBF: spatial coexpression analysis using Bayesian fused approaches in spatial omics datasets.GigaScience · 2026Article
- SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and visualization.GigaScience · 2026Article
- APM⁺ macrophages associated with plaque vulnerability via MIF-CD74 signaling: a multi-omics study.Human genomics · 2026Article
- Identification of programmed cell death-related subtypes reveals immune heterogeneity and therapeutic divergence in colon cancer.Theranostics · 2026Article
- The role of R-loop aberrations in lower-grade gliomas: prognostic, immune, and metabolic implications from multi-omics and machine learning analysis.Frontiers in immunology · 2026Article
- Integrating single-cell and spatial transcriptomics reveals glycolysis heterogeneity and NEK6-mediated progression in colorectal cancer.Frontiers in immunology · 2026Article
- Pan-cancer neural regulation pattern with implications for patient stratification and immunotherapy.Molecular therapy. Nucleic acids · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The expeditious growth in spatial omics technologies enables the profiling of genome-wide molecular events at molecular and single-cell resolution, highlighting a need for fast and reliable methods to characterize spatial patterns. We developed SpaGene, a model-free method to discover spatial patterns rapidly in large-scale spatial omics studies. Analyzing simulation and a variety of spatially resolved transcriptomics data showed that SpaGene is more powerful and scalable than existing methods. Spatial expression patterns identified by SpaGene reconstruct unobserved tissue structures. SpaGene also successfully discovers ligand-receptor interactions through their colocalization.
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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.