ArticleCell research2020
Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.
Article in Cell research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 99 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
99 citing papers in PubMed, 1 synthesis or guideline pooled it, 154 citations in OpenAlex.
- Engineered tissues and strategies to overcome challenges in drug development.Advanced drug delivery reviews · 2020Pooled it
- IGFBP5 derived from endothelial cells drive vascular invasion and liver metastasis of colorectal cancer by activating the ITGB3/PI3K/AKT Axis.Cell death & disease · 2026Article
- Identifying potential ligand-receptor interactions by integrating LSTM network and the attention mechanism for cell-cell communication prediction.Journal of translational medicine · 2026Article
- SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data.Genome biology · 2026Article
- Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.Nature communications · 2026Article
- Constructing the spatiotemporal atlas of single-cell lineage trajectories in stereotypic biological structures.iScience · 2026Article
- Single-Cell Sequencing Data Revealed Mechanisms of Interactions Between Tumor Cells and Cancer-Associated Fibroblasts in Metastatic Colorectal Cancer.BioMed research international · 2026Article
- A single-cell immune atlas of primary and secondary lymphoid organs in pigs.Frontiers in immunology · 2026Article
- Article
- Insights gained from single-cell sequencing analysis of ischemic stroke.Frontiers in cell and developmental biology · 2026Review
- Cell-cell interactions as predictive and prognostic markers for drug responses in cancer.Genome medicine · 2025Review
- Single-Cell RNA Sequencing Reveals the Critical Role of SEC16B in Lung Metastasis of Osteosarcoma.FASEB bioAdvances · 2025Article
- Systematic assessment of microenvironment-dependent transcriptional patterns and intercellular communication.Genome biology · 2025Article
- Multi-Transcriptomic Analysis Reveals GSC-Driven MES-Like Differentiation via EMT in GBM Cell-Cell Communication.Biomedicines · 2025Article
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Novel insights into kidney disease: the scRNA-seq and spatial transcriptomics approaches: a literature review.BMC nephrology · 2025Review
- Advances in Microfluidic Single-Cell RNA Sequencing and Spatial Transcriptomics.Micromachines · 2025Review
- CTCF enhances pancreatic cancer progression via FLG-AS1-dependent epigenetic regulation and macrophage polarization.Cell death and differentiation · 2025Article
- Transfer learning of multicellular organization via single-cell and spatial transcriptomics.PLoS computational biology · 2025Article
- Quantitative characterization of cell niches in spatially resolved omics data.Nature genetics · 2025Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized transcriptomic studies by providing unprecedented cellular and molecular throughputs, but spatial information of individual cells is lost during tissue dissociation. While imaging-based technologies such as in situ sequencing show great promise, technical difficulties currently limit their wide usage. Here we hypothesize that cellular spatial organization is inherently encoded by cell identity and can be reconstructed, at least in part, by ligand-receptor interactions, and we present CSOmap, a computational tool to infer cellular interaction de novo from scRNA-seq. We show that CSOmap can successfully recapitulate the spatial organization of multiple organs of human and mouse including tumor microenvironments for multiple cancers in pseudo-space, and reveal molecular determinants of cellular interactions. Further, CSOmap readily simulates perturbation of genes or cell types to gain novel biological insights, especially into how immune cells interact in the tumor microenvironment. CSOmap can be a widely applicable tool to interrogate cellular organizations based on scRNA-seq data for various tissues in diverse systems.
Indexed as
Identifiers
What OpenQuestion holds
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.