ArticleGenome biology2020
DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Integrated Multi-Omics Reveals Cellular States and Microenvironmental Remodeling in Coexisting DCIS and IDC.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Late-stage dedifferentiation and epigenetic memory of cancer stem cells in hepatocellular carcinoma.Journal of translational medicine · 2026Article
- Phylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA.Genome biology · 2026Article
- Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.Genome medicine · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- CluVar: clustering of variants using autoencoder for inferring cancer subclones from single cell RNA sequencing data.Briefings in bioinformatics · 2025Article
- Fast tumor phylogeny regression via tree-structured dual dynamic programming.Bioinformatics (Oxford, England) · 2025Article
- De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.Genome research · 2025Article
- Structure-guided integrative soft deep clustering analysis of scRNA-seq and scATAC-seq data.Frontiers in microbiology · 2025Article
- Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers.PloS one · 2025Article
- Neuroblastoma plasticity during metastatic progression stems from the dynamics of an early sympathetic transcriptomic trajectory.Nature communications · 2024Article
- De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.bioRxiv : the preprint server for biology · 2024Article
- Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis.Briefings in bioinformatics · 2024Article
- Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution.Nature communications · 2024Article
- Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution.Genome biology · 2024Article
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.NAR genomics and bioinformatics · 2024Article
- A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.Genome research · 2024Article
- A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity.Scientific data · 2024Article
- Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.PLoS computational biology · 2023Article
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Authors and funding
4 authors.
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Abstract
Although scRNA-seq is now ubiquitously adopted in studies of intratumor heterogeneity, detection of somatic mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones. DENDRO utilizes transcribed point mutations and accounts for technical noise and expression stochasticity. We benchmark DENDRO and demonstrate its application on simulation data and real data from three cancer types. In particular, on a mouse melanoma model in response to immunotherapy, DENDRO delineates the role of neoantigens in treatment response.
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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.