ArticleThe annals of applied statistics2021
ESTIMATION OF CELL LINEAGE TREES BY MAXIMUM-LIKELIHOOD PHYLOGENETICS.
Article in The annals of applied statistics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 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
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- 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
- Inferring cell differentiation maps from lineage tracing data.Nature methods · 2026Article
- ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing.Systematic biology · 2026Article
- Inferring Cell Differentiation Dynamics with Unobserved Progenitors.bioRxiv : the preprint server for biology · 2025Article
- 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
- Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.Nature genetics · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
CRISPR technology has enabled cell lineage tracing for complex multicellular organisms through insertion-deletion mutations of synthetic genomic barcodes during organismal development. To reconstruct the cell lineage tree from the mutated barcodes, current approaches apply general-purpose computational tools that are agnostic to the mutation process and are unable to take full advantage of the data's structure. We propose a statistical model for the CRISPR mutation process and develop a procedure to estimate the resulting tree topology, branch lengths, and mutation parameters by iteratively applying penalized maximum likelihood estimation. By assuming the barcode evolves according to a molecular clock, our method infers relative ordering across parallel lineages, whereas existing techniques only infer ordering for nodes along the same lineage. When analyzing transgenic zebrafish data from McKenna, Findlay and Gagnon et al. (2016), we find that our method recapitulates known aspects of zebrafish development and the results are consistent across samples.
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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 OpenQuestion graph.