ArticlePLoS computational biology2024
Scuphr: A probabilistic framework for cell lineage tree reconstruction.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Phylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA.Genome biology · 2026Article
- Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo.Nature communications · 2021Article
- Eleven grand challenges in single-cell data science.Genome biology · 2020Review
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Authors and funding
4 authors.
Funding
Abstract
Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method's robustness is investigated using various synthetic datasets and a biological dataset of 18 cells.
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Registered trials
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