ArticleNature communications2026
SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.
Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed.
- Article
- Article
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- A comparison between CARLIN and DNA Typewriter in CRISPR-mediated lineage tracing.BMC bioinformatics · 2026Article
- Age-dependent Phylodynamics with Application to Single-cell Lineage Trees.Molecular biology and evolution · 2026Article
- VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
CRISPR-based lineage tracing offers a promising avenue to decipher single-cell lineage trees, especially in organisms not amenable to microscopy. Sequential genome editing records not only genetic edits but also the order in which they occur. To leverage this enriched information, we introduce SciPhy, a simulation and inference tool implemented in BEAST 2. SciPhy utilizes a Bayesian phylogenetic approach to jointly estimate time-scaled phylogenies and cell population parameters. After validation on simulated data, we use simulated and real data from a monoclonal cell culture to benchmark SciPhy against existing methods and find that it consistently reconstructs more accurate phylogenies. Compared to UPGMA, SciPhy additionally reports uncertainty and proliferation rates. Our second example applies SciPhy to murine gastruloids, demonstrating its ability to model time-varying population dynamics in early development. Together, these results establish a phylodynamic framework for the quantitative analysis of lineage tracing data. SciPhy's codebase is publicly available at https://github.com/azwaans/SciPhy .
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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 Socratic graph.