ArticleNature methods2018
Mapping the physical network of cellular interactions.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 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
98 citing papers in PubMed, 155 citations in OpenAlex.
- Resolving cell-cell interaction networks and their molecular logic in complex tissues.Nature methods · 2026Article
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Artificial intelligence in spatial transcriptomics: a review of methods, datasets, and directions.Briefings in bioinformatics · 2026Review
- Decoding Immune Cell Doublets in Humans: From Artifacts to Insights.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2026Review
- T Cell-Macrophage Interactions Influence Chemotherapeutic Response in Ovarian Cancer Patients.International journal of molecular sciences · 2026Article
- CAGNet: a structure-aware clustering-alternated graph network for cell-cell interaction inference in spatial transcriptomics.BMC bioinformatics · 2026Article
- Informed spatially aware patterns for multiplexed immunofluorescence data.Scientific reports · 2026Article
- Spider: a flexible and unified framework for simulating spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- DeepPNCC: reconstructing pseudo-spatial cell-cell interaction landscapes from single-cell data to decipher breast cancer pathogenesis.Journal of translational medicine · 2025Article
- Cell-cell interactions as predictive and prognostic markers for drug responses in cancer.Genome medicine · 2025Review
- Article
- Ultra-high-scale cytometry-based cellular interaction mapping.Nature methods · 2025Article
- Direct cell interactions potentially regulate transcriptional programmes that control the responses of high grade serous ovarian cancer patients to therapy.Scientific reports · 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
- Article
- Across the space: applications of spatial transcriptomic technology in healthy and diseased muscle.Frontiers in cell and developmental biology · 2025Review
- ULMnet: inferring physical cell-cell communication networks from scRNAseq data using univariate linear models.Frontiers in immunology · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Opportunities and challenges in the application of spatiotemporal transcriptomics in plant research.Frontiers in plant science · 2025Review
38 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A cell's function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network based on physical cell interaction and single-cell mRNA sequencing, and show that it can be used to discover new preferential cellular interactions without prior knowledge of component cell types. ProximID found specific interactions between megakaryocytes and mature neutrophils and between plasma cells and myeloblasts and/or promyelocytes (precursors of neutrophils) in mouse bone marrow, and it identified a Tac1
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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.