ArticleNature methods2016
Clonal genotype and population structure inference from single-cell tumor sequencing.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder.Genome biology · 2025Article
- Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.Nature communications · 2025Article
- Article
- A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data.Genome research · 2024Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data.Genome research · 2023Article
- Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.PLoS computational biology · 2023Article
- Assessing the performance of methods for cell clustering from single-cell DNA sequencing data.PLoS computational biology · 2023Article
- Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.Nature communications · 2023Article
- Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer.Nature communications · 2023Article
- Review
- RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data.Frontiers in genetics · 2023Article
- Improving cellular phylogenies through the integrated use of mutation order and optimality principles.Computational and structural biotechnology journal · 2023Article
- bmVAE: a variational autoencoder method for clustering single-cell mutation data.Bioinformatics (Oxford, England) · 2023Article
- CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data.Genome biology · 2022Article
- Advances in Single-Cell Sequencing Technology and Its Applications in Triple-Negative Breast Cancer.Breast cancer (Dove Medical Press) · 2022Review
- SCClone: Accurate Clustering of Tumor Single-Cell DNA Sequencing Data.Frontiers in genetics · 2022Article
- MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells.Frontiers in genetics · 2022Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic counts as well as false genotype measurements owing to the sequencing of multiple cells. We describe the Single Cell Genotyper (https://bitbucket.org/aroth85/scg), an open-source software based on a statistical model coupled with a mean-field variational inference method, which can be used to address these problems and robustly infer clonal genotypes.
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Registered trials
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.