ArticleCell systems2023
Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing.
Article in Cell systems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 32 citations in OpenAlex.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis.Nature genetics · 2026Article
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 2026Article
- 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
- Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.Cell genomics · 2026Article
- Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining.Genome research · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- A method for CRISPR/Cas9-induced genetic barcoding and lineage tracing in sheep.Scientific reports · 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
- Integrative Inference of Spatially Resolved Cell Lineage Trees using LineageMap.bioRxiv : the preprint server for biology · 2026Article
- Inferring Cell Differentiation Dynamics with Unobserved Progenitors.bioRxiv : the preprint server for biology · 2025Article
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- CLADES: a hybrid NeuralODE-Gillespie approach for unveiling clonal cell fate and differentiation dynamics.Nature communications · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML.Genome biology · 2025Article
- The lives of cells, recorded.Nature reviews. Genetics · 2025Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
CRISPR-Cas9-based genome editing combined with single-cell sequencing enables the tracing of the history of cell divisions, or cellular lineage, in tissues and whole organisms. Although standard phylogenetic approaches may be applied to reconstruct cellular lineage trees from this data, the unique features of the CRISPR-Cas9 editing process motivate the development of specialized models that describe the evolution of CRISPR-Cas9-induced mutations. Here, we introduce the "star homoplasy" evolutionary model that constrains a phylogenetic character to mutate at most once along a lineage, capturing the "non-modifiability" property of CRISPR-Cas9 mutations. We derive a combinatorial characterization of star homoplasy phylogenies and use this characterization to develop an algorithm, "Startle", that computes a maximum parsimony star homoplasy phylogeny. We demonstrate that Startle infers more accurate phylogenies on simulated lineage tracing data compared with existing methods and finds parsimonious phylogenies with fewer metastatic migrations on lineage tracing data from mouse metastatic lung adenocarcinoma.
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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.