ArticleGenome research2021
Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders.
Article in Genome research, 2021. 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.
- TALE and Hox Transcription Factors Modulate Adult Behaviors in Zebrafish.Behavior genetics · 2026Article
- Decomposing the genetic risk of autism spectrum disorder into discrete molecular subtypes underlie clinical heterogeneity based on transcriptome profile.Journal of translational medicine · 2026Article
- Trisomy 21 Drives ADARB1 Overexpression and Premature RNA Recoding in the Developing Fetal Brain.Nature communications · 2026Article
- TALE and Hox Transcription Factors Control Adult Behaviors in Zebrafish.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic Analysis of the Amygdala in Subjects with Schizophrenia, Bipolar Disorder and Major Depressive Disorder Reveals Differentially Altered Metabolic Pathways.Schizophrenia bulletin · 2026Article
- Discovering disease genetic variation impacting gene expression in 103 brain tissues with the Brain Ontology Expression (BRONTE) graph neural network model.bioRxiv : the preprint server for biology · 2025Article
- Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data.Genomics, proteomics & bioinformatics · 2025Article
- lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression.BMC genomics · 2025Article
- Article
- Multiomic single-cell profiling identifies critical regulators of postnatal brain.Nature genetics · 2025Article
- Differentially Altered Metabolic Pathways in the Amygdala of Subjects with Schizophrenia, Bipolar Disorder and Major Depressive Disorder.medRxiv : the preprint server for health sciences · 2024Article
- Article
- deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues.Genomics, proteomics & bioinformatics · 2023Article
- Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data.bioRxiv : the preprint server for biology · 2023Article
- Cell-Type-Specific Profibrotic Scores across Multi-Organ Systems Predict Cancer Prognosis.Cancers · 2021Article
- DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner.Nucleic acids research · 2021Article
- Article
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Authors and funding
6 authors.
Funding
Abstract
As the most complex organ of the human body, the brain is composed of diverse regions, each consisting of distinct cell types and their respective cellular interactions. Human brain development involves a finely tuned cascade of interactive events. These include spatiotemporal gene expression changes and dynamic alterations in cell-type composition. However, our understanding of this process is still largely incomplete owing to the difficulty of brain spatiotemporal transcriptome collection. In this study, we developed a tensor-based approach to impute gene expression on a transcriptome-wide level. After rigorous computational benchmarking, we applied our approach to infer missing data points in the widely used BrainSpan resource and completed the entire grid of spatiotemporal transcriptomics. Next, we conducted deconvolutional analyses to comprehensively characterize major cell-type dynamics across the entire BrainSpan resource to estimate the cellular temporal changes and distinct neocortical areas across development. Moreover, integration of these results with GWAS summary statistics for 13 brain-associated traits revealed multiple novel trait-cell-type associations and trait-spatiotemporal relationships. In summary, our imputed BrainSpan transcriptomic data provide a valuable resource for the research community and our findings help further studies of the transcriptional and cellular dynamics of the human brain and related diseases.
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