ArticleBioinformatics (Oxford, England)2025
Single-cell copy number calling and event history reconstruction.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- LeafRank: A phylodynamic framework for inferring relative fitness from single-cell phylogenies in chromosomally unstable tumors.bioRxiv : the preprint server for biology · 2026Article
- A tumor profiling resource for ovarian cancer: insights into chemotherapy-driven heterogeneity and personalized treatment strategy.Nature communications · 2026Article
- Phylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA.Genome biology · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- SoMaCX: a complex generative genome modeling framework.BMC genomics · 2025Article
- Feasibility of multiomics tumor profiling for guiding treatment of melanoma.Nature medicine · 2025Observational
- Bayesian inference of fitness landscapes via tree-structured branching processes.Bioinformatics (Oxford, England) · 2025Article
- De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.Genome research · 2025Article
- CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling.Genome biology · 2025Article
- Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.bioRxiv : the preprint server for biology · 2024Article
- Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia.Nature communications · 2024Article
- SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- Oncotree2vec - a method for embedding and clustering of tumor mutation trees.Bioinformatics (Oxford, England) · 2024Article
- NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model.Algorithms for molecular biology : AMB · 2024Article
- CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data.Briefings in bioinformatics · 2024Article
- scAbsolute: measuring single-cell ploidy and replication status.Genome biology · 2024Article
- A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data.Genome research · 2024Article
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5 authors.
Funding
Abstract
motivationCopy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolution for copy number profiling down to the level of individual cells. Recent high-throughput protocols allow for the processing of hundreds of cells through shallow whole-genome DNA sequencing. The resulting low read-depth data poses substantial statistical and computational challenges to the identification of copy number alterations.
resultsWe developed SCICoNE, a statistical model and MCMC algorithm tailored to single-cell copy number profiling from shallow whole-genome DNA sequencing data. SCICoNE reconstructs the history of copy number events in the tumour and uses these evolutionary relationships to identify the copy number profiles of the individual cells. We show the accuracy of this approach in evaluations on simulated data and demonstrate its practicability in applications to two breast cancer samples from different sequencing protocols. AVAILABILITY AND IMPLEMENTATION: SCICoNE is available at https://github.com/cbg-ethz/SCICoNE.
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