ArticleNature biotechnology2024
Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Single-cell multi-omics dissects transcript isoform and immune repertoire dynamics in human immunosenescence.Science China. Life sciences · 2026Article
- In vivo effect of anti-PD-1 on HIV-specific CD8+T-cells in men with HIV.Nature communications · 2026Article
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- ABO: A 3D stroma-supported culture platform enabling full human B-lymphopoiesis for disease modeling and gene therapy development.Cell reports. Medicine · 2026Article
- Ganoderma lucidum spore powder enhances IFN-α-mediated antiviral capacity of COVID-19 vaccine boosters revealed by single-cell multi-omics sequencing.Journal of advanced research · 2026Article
- A temporal map of B cell diversification mechanisms in mice.Nature immunology · 2026Article
- Competing gene regulatory networks drive naive and memory B cell differentiation.Molecular systems biology · 2026Article
- Statistical Methods for Detecting Nonlinear Relationships in Gene Expression and Omics Data: A Review.International journal of molecular sciences · 2026Review
- circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics.Genome medicine · 2026Article
- Congenital cytomegalovirus infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine.MethodsX · 2026Article
- Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics.Immune network · 2026Review
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- IFN-gene signatures in B cells following influenza A and B virus infection and influenza vaccination.EMBO molecular medicine · 2026Article
- Tissue-restricted secondary TCR engagement drives the transition from stem-like to CD200Nature immunology · 2026Article
- crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis.BMC genomics · 2026Article
- Spatial transcriptomic imaging of an intact organism using volumetric DNA microscopy.Nature biotechnology · 2026Article
- Childhood brain tumors instruct cranial hematopoiesis and immunotolerance.Nature genetics · 2026Article
- Multifaceted B cell response to transient HIV viremia in elite controllers.PLoS pathogens · 2026Article
- A non-canonical lymphoblast in refractory childhood T-cell leukaemia.Nature communications · 2025Article
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Authors and funding
12 authors.
Funding
Abstract
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion .
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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 OpenQuestion graph.