ArticleGenome biology2025
Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Integrative Transcriptomic Analysis Reveals Impaired Oligodendrocyte Maturation and Myelination Signature in the Hippocampus of a Murine Model of Neuropsychiatric Lupus.International journal of molecular sciences · 2026Article
- Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala.Addiction biology · 2026Article
- Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution.Cell reports methods · 2026Article
- Integration of Bulk and Single-Cell RNA Sequencing Analyses in Biomedicine.International journal of molecular sciences · 2026Review
- A transcriptomic dimension of neuronal and immune gene programs within the subgenual anterior cingulate cortex in schizophrenia.Translational psychiatry · 2026Article
- A guide to transcriptomic deconvolution in cancer.Nature reviews. Cancer · 2026Review
- omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.Genome biology · 2026Article
- Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala.bioRxiv : the preprint server for biology · 2025Article
- Cellular and molecular associations with intrinsic brain organization.Nature communications · 2025Article
- Article
- Cellular and molecular associations with intrinsic brain organization.bioRxiv : the preprint server for biology · 2025Article
- Transcriptomic Analysis of the Human Habenula in Schizophrenia.The American journal of psychiatry · 2025Article
- BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration.Genome biology · 2025Article
- An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus.Nature neuroscience · 2025Article
- lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression.BMC genomics · 2025Article
- Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons.Nature communications · 2025Article
- Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex.Genome biology · 2025Article
- Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species.iScience · 2025Article
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Abstract
Cellular deconvolution of bulk RNA-sequencing data using single cell/nuclei RNA-seq reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as the human brain. Here, we generate a multi-assay dataset in postmortem human dorsolateral prefrontal cortex from 22 tissue blocks, including bulk RNA-seq, reference snRNA-seq, and orthogonal measurement of cell type proportions with RNAScope/ImmunoFluorescence. We use this dataset to evaluate six deconvolution algorithms. Bisque and hspe were the most accurate methods. The dataset, as well as the Mean Ratio gene marker finding method, is made available in the DeconvoBuddies R/Bioconductor package.
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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 Socratic graph.