ArticleNature communications2020
Accurate estimation of cell composition in bulk expression through robust integration of single-cell information.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 317 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
317 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Identifying novel gene dysregulation associated with opioid overdose death: a meta-analysis of differential gene expression in human prefrontal cortex.Translational psychiatry · 2026Pooled it
- Gene expression differences associated with alcohol use disorder in human brain.Molecular psychiatry · 2025Pooled it
- Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2027Review
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- CDState Resolves Malignant Cell Heterogeneity from Bulk Tumor RNA Sequencing Data.Cancer research · 2026Article
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- CellMAGE: cell-type deconvolution for multi-parent population analysis of gene expression.bioRxiv : the preprint server for biology · 2026Article
- Progressive hypothalamic neuroinflammation in ovariectomized mice parallels aging-related transcriptomic changes in the female human hypothalamus.JCI insight · 2026Article
- Regional signaling controls stem cell-mediated regeneration in an invertebrate chordate.PLoS biology · 2026Article
- DeOPUS: cellular deconvolution via optimized power-transformed unmixing with shrinkage.Briefings in bioinformatics · 2026Article
- Spatial and single-cell profiling identify NDRG1⁺ macrophages as key hallmark of angiogenic remodeling and platinum resistance in HGSOC.Translational oncology · 2026Article
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- Mapping genetic regulation of gene expression to cellular contexts identifies long non-coding RNAs associated with brain disorders.Nature communications · 2026Article
- 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
- Genome-wide pQTL mapping in human skin identifies specific genetic regulators and mechanistic links to skin disorders.Nature communications · 2026Article
- Integrated inference of cellular compositions and gene expression programs by deconvolution.Cell regeneration (London, England) · 2026Article
- Single-cell and spatial omics in liver identify cell-cell communication regulators in aging and insulin resistance.Metabolism: clinical and experimental · 2026Article
- cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution.Nature communications · 2026Article
- Carotid plaque macrophage burden and inflammatory lipid-associated macrophage markers predict secondary major adverse cardiovascular events after endarterectomy.European heart journal · 2026Article
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.Nature biotechnology · 2026Article
257 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
Abstract
We present Bisque, a tool for estimating cell type proportions in bulk expression. Bisque implements a regression-based approach that utilizes single-cell RNA-seq (scRNA-seq) or single-nucleus RNA-seq (snRNA-seq) data to generate a reference expression profile and learn gene-specific bulk expression transformations to robustly decompose RNA-seq data. These transformations significantly improve decomposition performance compared to existing methods when there is significant technical variation in the generation of the reference profile and observed bulk expression. Importantly, compared to existing methods, our approach is extremely efficient, making it suitable for the analysis of large genomic datasets that are becoming ubiquitous. When applied to subcutaneous adipose and dorsolateral prefrontal cortex expression datasets with both bulk RNA-seq and snRNA-seq data, Bisque replicates previously reported associations between cell type proportions and measured phenotypes across abundant and rare cell types. We further propose an additional mode of operation that merely requires a set of known marker genes.
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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.