ArticleNature biotechnology2023
Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers, 1 of them a synthesis that pooled it.
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Who cites it
117 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Contribution of germline and somatic mutations to risk of neuromyelitis optica spectrum disorder.Cell genomics · 2025Pooled it
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- Deeper response predicts better outcomes in high-risk-smoldering-myeloma: results of the I-PRISM phase II clinical trial.Nature communications · 2025Trial
- Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer.Cancer discovery · 2024Trial
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Asynchronous Evolution of Epithelium and Stroma Differentiates Precursor Lesions from Pancreatic Cancer.Cancer discovery · 2026Article
- Pervasive Somatic Mutations inbioRxiv : the preprint server for biology · 2026Article
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- Benchmarking copy number alteration inference methods for spatial transcriptomics.Nature communications · 2026Article
- Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.Nature genetics · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Hematopoietic mosaic chromosomal alterations are pleiotropic drivers of inflammaging, multimorbidity, and mortality.medRxiv : the preprint server for health sciences · 2026Article
- Adherent-to-suspension transition modulates circulating tumor cell dynamics and metastatic potential in melanoma.Molecules and cells · 2026Article
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- Fibroblast-like cells in mesothelioma can derive from tumor cells.Cell death and differentiation · 2026Article
- Full-Body AI Agent: A Perspective on Multi-Scale Collaborative AI for Systemic Biology and Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.Briefings in bioinformatics · 2026Article
57 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq) has the potential to investigate both genetic and nongenetic sources of tumor heterogeneity in a single assay. Here we present a computational method, Numbat, that integrates haplotype information obtained from population-based phasing with allele and expression signals to enhance detection of copy number variations from scRNA-seq. Numbat exploits the evolutionary relationships between subclones to iteratively infer single-cell copy number profiles and tumor clonal phylogeny. Analysis of 22 tumor samples, including multiple myeloma, gastric, breast and thyroid cancers, shows that Numbat can reconstruct the tumor copy number profile and precisely identify malignant cells in the tumor microenvironment. We identify genetic subpopulations with transcriptional signatures relevant to tumor progression and therapy resistance. Numbat requires neither sample-matched DNA data nor a priori genotyping, and is applicable to a wide range of experimental settings and cancer types.
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