ArticleNature communications2024
Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Effects of SSRIs on the spatial transcriptome of dorsal raphe serotonin neurons.Molecular psychiatry · 2026Article
- Neuron type-specific translatomes in dorsal hippocampus during early memory consolidation.Nature communications · 2026Article
- Spatial transcriptomic profiling uncovers the molecular effects of the neurotoxicant polychlorinated biphenyls (PCBs) in the brains of adult mice.Molecular psychiatry · 2026Article
- Uncovering the Key Circuit FOSL2/FOS/EGR3/EGR1, Contributing to the Hyperexcitability of Excitatory Neurons in the Epileptic Temporal Cortex and Hippocampus.International journal of molecular sciences · 2026Article
- Single-cell resolution spatial transcriptomic signature of the retrosplenial cortex during memory consolidation.Molecular psychiatry · 2026Article
- Spatial transcriptomics reveals brain-wide circadian disruption in an Alzheimer's disease model.bioRxiv : the preprint server for biology · 2026Article
- Distinct mechanisms of transcriptomic habituation to repeated stress in the mouse hippocampus.Nature communications · 2025Article
- Discovery and validation of RAB3B as a diagnostic biomarker for prostate cancer with serum PSA below 10 ng/mL based on a multi-omics study.Cancer cell international · 2025Article
- Systematically Revealing Quantitative Multi-Target Integrative Effects of Plants With Artificial Intelligence Method.Plant biotechnology journal · 2025Article
- Immediate-early genes Arc and c-Fos show divergent brain-wide expression following contextual fear conditioning.Communications biology · 2025Article
- Neuron type-specific mRNA translation programs provide a gateway for memory consolidation.bioRxiv : the preprint server for biology · 2025Article
- The psychoplastogen tabernanthalog induces neuroplasticity without proximate immediate early gene activation.Nature neuroscience · 2025Article
- Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration.eLife · 2025Article
- Single-cell technology grows up: Leveraging high-resolution omics approaches to understand neurodevelopmental disorders.Current opinion in neurobiology · 2025Review
- The gene expression signature of electrical stimulation in the human brain.bioRxiv : the preprint server for biology · 2024Article
- Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation.Nature communications · 2023Article
- Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation.bioRxiv : the preprint server for biology · 2023Article
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11 authors.
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Abstract
Neuronal activity-dependent transcription directs molecular processes that regulate synaptic plasticity, brain circuit development, behavioral adaptation, and long-term memory. Single cell RNA-sequencing technologies (scRNAseq) are rapidly developing and allow for the interrogation of activity-dependent transcription at cellular resolution. Here, we present NEUROeSTIMator, a deep learning model that integrates transcriptomic signals to estimate neuronal activation in a way that we demonstrate is associated with Patch-seq electrophysiological features and that is robust against differences in species, cell type, and brain region. We demonstrate this method's ability to accurately detect neuronal activity in previously published studies of single cell activity-induced gene expression. Further, we applied our model in a spatial transcriptomic study to identify unique patterns of learning-induced activity across different brain regions in male mice. Altogether, our findings establish NEUROeSTIMator as a powerful and broadly applicable tool for measuring neuronal activation, whether as a critical covariate or a primary readout of interest.
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