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September 12, 2025Open Access

Phylogenetic tree inference from single-cell RNA sequencing data

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Authors

NZNorio ZimmermannXSXiaoyu SunJHJoanna Hård

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Overview

Novel method reconstructs phylogenetic relationships in cancer cells using single-cell RNA sequencing data, suggesting insights into tumor evolution.

Key Points

  • Phylogenetic inference from single-cell RNA sequencing improves understanding of tumor evolution and treatment resistance.
  • The novel method uses maximum likelihood and random-scan greedy search for tree reconstruction.
  • Dynamic switching between cell lineage and mutation tree representations helps overcome local optima.
  • Demonstrated superior performance on simulated data, with applicability to real cancer sequencing data.

Cite This Study

Zimmermann et al. (2025) studied this question.

synapsesocial.com/papers/68d44c4631b076d99fa55ad2https://doi.org/10.1101/2025.09.04.674140
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Also Consider

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  1. 1Canopy2: tumor phylogeny inference by bulk DNA and single-cell RNA sequencing2024 · 1 citations
  2. 2Scuphr: A probabilistic framework for cell lineage tree reconstruction2024 · 3 citations
  3. 3DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data2025
  4. 4STAR: ultrafast universal RNA-seq aligner2012 · 58,263 citations
  5. 5Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics2023 · 24 citations