ArticleProceedings. Biological sciences2022
TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data.
Article in Proceedings. Biological sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Can you trust your reconstructed lineage tree? A homoplasy-based approach for irreversible evolution.bioRxiv : the preprint server for biology · 2026Article
- LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage trees.Bioinformatics (Oxford, England) · 2026Article
- SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.Nature communications · 2026Article
- Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.Cell genomics · 2026Article
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining.Genome research · 2026Article
- Age-dependent Phylodynamics with Application to Single-cell Lineage Trees.Molecular biology and evolution · 2026Article
- LAML-Pro: Joint Maximum Likelihood Inference of Cell Genotypes and Cell Lineage Trees.bioRxiv : the preprint server for biology · 2026Article
- VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies.bioRxiv : the preprint server for biology · 2026Article
- ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing.Systematic biology · 2026Article
- TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.bioRxiv : the preprint server for biology · 2025Article
- ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing.bioRxiv : the preprint server for biology · 2025Article
- Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML.Genome biology · 2025Article
- Detecting branching rate heterogeneity with tree balance statistics in lineage tracing trees.bioRxiv : the preprint server for biology · 2025Article
- The lives of cells, recorded.Nature reviews. Genetics · 2025Review
- A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Punctuational evolution is pervasive in distal site metastatic colonization.Proceedings. Biological sciences · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The development of organisms and tissues is dictated by an elaborate balance between cell division, apoptosis and differentiation: the cell population dynamics. To quantify these dynamics, we propose a phylodynamic inference approach based on single-cell lineage recorder data. We developed a Bayesian phylogenetic framework-time-scaled developmental trees (TiDeTree)-that uses lineage recorder data to estimate time-scaled single-cell trees. By implementing TiDeTree within BEAST 2, we enable joint inference of the time-scaled trees and the cell population dynamics. We validated TiDeTree using simulations and showed that performance further improves when including multiple independent sources of information into the inference, such as frequencies of editing outcomes or experimental replicates. We benchmarked TiDeTree against state-of-the-art methods and show comparable performance in terms of tree topology, plus direct assessment of uncertainty and co-estimation of additional parameters. To demonstrate TiDeTree's use in practice, we analysed a public dataset containing lineage data from approximately 100 stem cell colonies. We estimated a time-scaled phylogeny for each colony; as well as the cell division and apoptosis rates underlying the growth dynamics of all colonies. We envision that TiDeTree will find broad application in the analysis of single-cell lineage tracing data, which will improve our understanding of cellular processes during development.
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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 OpenQuestion graph.