ArticleGenome biology2022
SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing 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 14 papers.
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Who cites it
14 citing papers in PubMed, 17 citations in OpenAlex.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Phylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA.Genome biology · 2026Article
- Estimating the Growth Rate of a Birth and Death Process Using data From a Small Sample.Bulletin of mathematical biology · 2026Article
- DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data.Genome biology · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.Nature communications · 2024Article
- Article
- Application and research progress of single cell sequencing technology in leukemia.Frontiers in oncology · 2024Review
- 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
- Single-cell phylogenies reveal changes in the evolutionary rate within cancer and healthy tissues.Cell genomics · 2023Article
- cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory.Bioinformatics (Oxford, England) · 2023Article
- Phylogenetic inference from single-cell RNA-seq data.Scientific reports · 2023Article
- SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.Genome biology · 2022Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present SIEVE, a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from single-cell DNA sequencing. SIEVE leverages raw read counts for all nucleotides and corrects the acquisition bias of branch lengths. In our simulations, SIEVE outperforms other methods in phylogenetic reconstruction and variant calling accuracy, especially in the inference of homozygous variants. Applying SIEVE to three datasets, one for triple-negative breast (TNBC), and two for colorectal cancer (CRC), we find that double mutant genotypes are rare in CRC but unexpectedly frequent in the TNBC samples.
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