ArticleMolecular systems biology2014
Digital cell quantification identifies global immune cell dynamics during influenza infection.
Article in Molecular systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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82 citing papers in PubMed.
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- Hypoxia inducible factors regulate pneumovirus replication by enhancing innate immune sensing.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Characterization, immune cell phenotyping and differential gene expression analysis of brain metastases and primary breast cancer samples.Scientific reports · 2026Article
- IFITM3 deficiency drives SARS-CoV-2 adaptation while preserving variant-specific traits.Nature communications · 2026Article
- Identification of the body fluid donors from mixture stains using bulk transcriptomes data.Briefings in bioinformatics · 2025Article
- TIMER3: an enhanced resource for tumor immune analysis.Nucleic acids research · 2025Article
- An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data.Nature communications · 2025Article
- HIDE: hierarchical cell-type deconvolution.Bioinformatics (Oxford, England) · 2025Article
- Optimized RNA sequencing deconvolution illustrates the impact of obesity and weight loss on cell composition of human adipose tissue.Obesity (Silver Spring, Md.) · 2025Article
- Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data.Briefings in bioinformatics · 2025Article
- EMixed: Probabilistic Multi-Omics Cellular Deconvolution of Bulk Omics Data.Journal of data science : JDS · 2025Article
- Alleviating batch effects in cell type deconvolution with SCCAF-D.Nature communications · 2024Article
- Targeting NTRK1 Enhances Immune Checkpoint Inhibitor Efficacy in NTRK1 Wild-Type Non-Small Cell Lung Cancer.Cancer research · 2024Article
- Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline.Briefings in bioinformatics · 2024Article
- Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data.Cell reports methods · 2024Article
- Characterization of driver mutations identifies gene signatures predictive of prognosis and treatment sensitivity in multiple myeloma.The oncologist · 2024Article
- Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice.Biology of sex differences · 2024Article
- Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data.bioRxiv : the preprint server for biology · 2024Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
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Abstract
Hundreds of immune cell types work in coordination to maintain tissue homeostasis. Upon infection, dramatic changes occur with the localization, migration, and proliferation of the immune cells to first alert the body of the danger, confine it to limit spreading, and finally extinguish the threat and bring the tissue back to homeostasis. Since current technologies can follow the dynamics of only a limited number of cell types, we have yet to grasp the full complexity of global in vivo cell dynamics in normal developmental processes and disease. Here, we devise a computational method, digital cell quantification (DCQ), which combines genome-wide gene expression data with an immune cell compendium to infer in vivo changes in the quantities of 213 immune cell subpopulations. DCQ was applied to study global immune cell dynamics in mice lungs at ten time points during 7 days of flu infection. We find dramatic changes in quantities of 70 immune cell types, including various innate, adaptive, and progenitor immune cells. We focus on the previously unreported dynamics of four immune dendritic cell subtypes and suggest a specific role for CD103(+) CD11b(-) DCs in early stages of disease and CD8(+) pDC in late stages of flu infection.
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