ArticleScientific reports2022
Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers, 2 of them syntheses that pooled it.
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Who cites it
108 citing papers in PubMed, 2 syntheses or guidelines pooled it, 132 citations in OpenAlex.
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- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- Targeting KIT prevents brain arteriovenous malformations driven by ALK1-deficient angiogenic endothelial cells.The Journal of clinical investigation · 2026Article
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- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- A single-cell atlas of porcine hematopoietic development.Nature communications · 2026Article
- Identifying condition-related cell-cell communication events using supervised tensor analysis.American journal of human genetics · 2026Article
- Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens.Neuron · 2026Article
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- Targeting the HMGB1-IL32 pathway to alleviate T cell exhaustion in epithelial ovarian cancer.GeroScience · 2026Article
- Identifying potential ligand-receptor interactions by integrating LSTM network and the attention mechanism for cell-cell communication prediction.Journal of translational medicine · 2026Article
- NOD2 activation reprograms infiltrating inflammatory monocytes in the Zika virus infected CNS to maintain neural correlates of learning and memory.bioRxiv : the preprint server for biology · 2026Article
- A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.Cell reports. Medicine · 2026Article
- Immune landscape of the affected brain in Rasmussen encephalitis.Scientific reports · 2026Article
- iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.Signal transduction and targeted therapy · 2026Article
- CAPTAIN: a multimodal foundation model pretrained on co-assayed single-cell RNA and protein.Nature communications · 2026Article
- Vascular Endothelial Growth Factor-D Improves Lung Vascular Integrity During Acute Lung Injury.Circulation research · 2026Article
- SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
48 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major computational and epistemological challenges. Here, we present Connectome, a software package for R which facilitates rapid calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Connectome can be used with any reference set of known ligand-receptor mechanisms. It has built-in functionality to facilitate differential and comparative connectomics, in which signaling networks are compared between tissue systems. Connectome focuses on computational and graphical tools designed to analyze and explore cell-cell connectivity patterns across disparate single-cell datasets and reveal biologic insight. We present approaches to quantify focused network topologies and discuss some of the biologic theory leading to their design.
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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.