ArticleNature communications2023
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 71 citations in OpenAlex.
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- Single-cell and spatial omics in liver identify cell-cell communication regulators in aging and insulin resistance.Metabolism: clinical and experimental · 2026Article
- Single-nucleus transcriptomics-based drug screening platform for focal cortical dysplasia.Molecular psychiatry · 2026Article
- Single-nucleus multiome shows motor neuron glutamate overactivation in amyotrophic lateral sclerosis.Brain : a journal of neurology · 2026Article
- Unraveling cell-cell communication through spatial transcriptomics: a review of computational methods.Briefings in bioinformatics · 2026Review
- Defective ventral neurogenesis due to midfetal Chd8 mutation drives autistic-like behavior in mice.Nature communications · 2026Article
- Deciphering molecular inputs to CRH neurons from POMC neurons.Fundamental research · 2026Article
- Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids.Nature communications · 2026Article
- A single-cell multiomic analysis identifies molecular and gene-regulatory mechanisms dysregulated in developing Down syndrome neocortex.Science (New York, N.Y.) · 2026Article
- Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids.Nature communications · 2026Article
- Integrated Single-Cell and System Network Analysis: Exploring Cellular Communication Network Complexity and Signal Transmission Dysregulation in Down Syndrome Brain.Neuroinformatics · 2026Article
- Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq.National science review · 2026Article
- Aberrant Splicing Signatures Underpin Oligodendrocyte Damage in ALS and Neuron Loss in FTD.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Spatially localized immune metaprograms reveal micro-niche organization in the human Dorsal Root Ganglion.PloS one · 2026Article
- Inferring spatial single-cell-level interactions through interpreting cell state and niche correlations learned by self-supervised graph transformer.Nature machine intelligence · 2026Article
- Metabolic reprogramming in sepsis-associated encephalopathy: emerging mechanisms, candidate biomarkers, and future therapeutic directions.Frontiers in medicine · 2026Review
- The Role of Metabolites in Cell-Cell Communication: A Review of Databases and Computational Tools.Cells · 2025Review
- CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.Nature protocols · 2025Review
- Intercellular signaling and synaptic deconstruction uncovered by single-cell and spatial transcriptomics in an AD tauopathy model.Communications biology · 2025Article
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5 authors at 1 institution in 1 country.
Funding
Abstract
Neural communication networks form the fundamental basis for brain function. These communication networks are enabled by emitted ligands such as neurotransmitters, which activate receptor complexes to facilitate communication. Thus, neural communication is fundamentally dependent on the transcriptome. Here we develop NeuronChat, a method and package for the inference, visualization and analysis of neural-specific communication networks among pre-defined cell groups using single-cell expression data. We incorporate a manually curated molecular interaction database of neural signaling for both human and mouse, and benchmark NeuronChat on several published datasets to validate its ability in predicting neural connectivity. Then, we apply NeuronChat to three different neural tissue datasets to illustrate its functionalities in identifying interneural communication networks, revealing conserved or context-specific interactions across different biological contexts, and predicting communication pattern changes in diseased brains with autism spectrum disorder. Finally, we demonstrate NeuronChat can utilize spatial transcriptomics data to infer and visualize neural-specific cell-cell communication.
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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.