ArticleGenome biology2022
CONET: copy number event tree model of evolutionary tumor history for single-cell data.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Inferring gene expression profiles of tumor clones.Bioinformatics (Oxford, England) · 2026Article
- LeafRank: A phylodynamic framework for inferring relative fitness from single-cell phylogenies in chromosomally unstable tumors.bioRxiv : the preprint server for biology · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
- Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data.Nucleic acids research · 2025Article
- Single-cell copy number calling and event history reconstruction.Bioinformatics (Oxford, England) · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments.GigaScience · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- 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
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.NAR genomics and bioinformatics · 2024Article
- Article
- A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data.Genome research · 2024Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.PLoS computational biology · 2023Article
- CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples.Genome biology · 2023Article
- A zero-agnostic model for copy number evolution in cancer.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an efficient, regularized MCMC procedure to search the space of possible model structures and parameters. We introduce a range of model priors and penalties for efficient regularization. CONET reveals copy number evolution in two breast cancer samples, and outperforms other methods in tree reconstruction, breakpoint identification and copy number calling.
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