ReviewNature reviews. Genetics2021
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.
Review in Nature reviews. Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 641 papers.
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
641 citing papers in PubMed.
- Disulfidptosis-based cancer therapy: Opportunity and challenge.Genes & diseases · 2027Review
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Resolving cell-cell interaction networks and their molecular logic in complex tissues.Nature methods · 2026Article
- Multi‑omics insights into uveitis: From mechanisms to precision medicine (Review).International journal of molecular medicine · 2026Review
- Characterizing intra- and intertumor heterogeneity in ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics.Genome research · 2026Article
- A Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities and Immune Architecture.Cancer discovery · 2026Article
- Integrated Multi-Omics Reveals Cellular States and Microenvironmental Remodeling in Coexisting DCIS and IDC.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- GPCR heteromers: Beyond the monomeric paradigm in neuropsychiatric drug discovery.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026Review
- Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics.Nature biotechnology · 2026Article
- Decoding Skeletal Biology Through Transcriptomics: Insights from Bulk, Single-Cell, Spatial, and Multi-Omics Approaches.International journal of molecular sciences · 2026Review
- Microenvironment-aware transcriptome reconstruction in spatial transcriptomics.Nature communications · 2026Article
- Single-cell and spatial transcriptomics reveal SUV39H1 as a master epigenetic driver of immunosuppressive niche and stemness in bladder cancer.Translational oncology · 2026Article
- Spatial Transcriptomics-Inspired Targeted Hydrogel for Dental Pulp Therapy via Strengthen Macrophage Communication.Advanced healthcare materials · 2026Article
- Stemness plasticity in hepatocellular carcinoma: spatial niches and therapeutic implications.Journal of liver cancer · 2026Article
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Proteomic insights into azoospermia: protein differences in testicular tissue between non-obstructive and obstructive azoospermia patients.Asian journal of andrology · 2026Article
- Glutathione metabolism-linked ferroptosis in human seminoma: a spatial multi-omics mapping study.Redox biology · 2026Article
- ProST: an image prompt-guided multimodal representation learning framework for spatial domain identification.Bioinformatics (Oxford, England) · 2026Article
- Stroma-Dominant Colorectal Cancer Harbors CAF-Rich Spatial Architecture and EMT-Associated Cancer Cell Plasticity Detectable After Dissemination.Biomolecules · 2026Article
581 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.
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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.