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July 30, 2025Open Access

Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution

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Authors

PZPini ZilberSPSebastian PrilloUniversity of California, BerkeleyNYNir YosefBerkeley College

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Overview

This research demonstrates a new homoplasy-based approach to assess lineage tree reliability in cell lineages, suggesting improved outcomes over traditional parsimony methods.

Key Points

  • The study presents a method to assess the reliability of inferred lineage trees despite lacking ground truth.
  • Simulations show that the homoplasy-based score effectively identifies accurate lineage reconstructions.
  • The proposed approach leverages the non-modifiability of Cas9-induced mutations for phylogenetic analysis.
  • Findings indicate that the homoplasy score is more powerful than traditional parsimony scores, enhancing lineage analysis.

Cite This Study

Zilber et al. (2025) studied this question.

synapsesocial.com/papers/689a0945e6551bb0af8cefc7https://doi.org/10.1101/2025.07.27.667007
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Also Consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

  1. 1Theoretical estimates on the expected number of mutations needed to reconstruct clonal lineage trees2026
  2. 2Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining2024
  3. 3Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.2024
  4. 4Phylogenetic tree inference from single-cell RNA sequencing data2025
  5. 5Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data2024 · 4 citations