ArticleNature communications2023
A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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87 citing papers in PubMed.
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- Mitochondrial transcript abundance in breast cancer circulating tumour cells may reflect both blood-derived transcripts and biological heterogeneity.Clinical & experimental metastasis · 2026Article
- Chromosomal instability in cancer: sources, consequences and new therapeutic opportunities.Signal transduction and targeted therapy · 2026Review
- Benchmarking copy number alteration inference methods for spatial transcriptomics.Nature communications · 2026Article
- Transposable elements and homotypic niches drive immune dynamics and resistance in melanoma epigenetic-based immunotherapy.Science advances · 2026Article
- Cross-species transcriptomic integration reveals a MIRO1-mediated macrophage-T cell axis in glioma.Life science alliance · 2026Article
- Robust and generalizable CNV detection for single-cell sequencing assays.Nucleic acids research · 2026Article
- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- The MIRO1-BAX Complex Dictates Life and Death at the Mitochondrial Gate.bioRxiv : the preprint server for biology · 2026Article
- Stepwise Protocol for Alternative Splicing Analysis in Single-Cell SMART-Seq2 RNA-Seq Data.Bio-protocol · 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
- Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.Genome medicine · 2026Article
- Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner's Guide.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and spatial transcriptomics reveal TNF-α promotes glioblastoma proliferation and migration via CP-mediated KLF10 upregulation.Functional & integrative genomics · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- TUSCAN: Tumor segmentation and classification analysis in spatial transcriptomics.PLoS computational biology · 2026Article
27 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Single-cell RNA sequencing is the reference technology to characterize the composition of the tumor microenvironment and to study tumor heterogeneity at high resolution. Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of the clonal substructure of tumors from single-cell RNA-seq data. It uses a multichannel segmentation algorithm exploiting the assumption that all the cells in a given copy number clone share the same breakpoints. Thus, the smoothed expression profile of every individual cell constitutes part of the evidence of the copy number profile in each subclone. SCEVAN can automatically and accurately discriminate between malignant and non-malignant cells, resulting in a practical framework to analyze tumors and their microenvironment. We apply SCEVAN to datasets encompassing 106 samples and 93,322 cells from different tumor types and technologies. We demonstrate its application to characterize the intratumor heterogeneity and geographic evolution of malignant brain tumors.
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