ArticleGenome biology2025
Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease.bioRxiv : the preprint server for biology · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- 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
- 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
- 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
- Spatial transcriptomics and artificial intelligence: a scoping review of emerging applications in head and neck pathology.Head and neck pathology · 2026Article
- Inferring cell differentiation maps from lineage tracing data.Nature methods · 2026Article
- Inferring Cell Differentiation Dynamics with Unobserved Progenitors.bioRxiv : the preprint server for biology · 2025Article
- High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.Science (New York, N.Y.) · 2025Article
- Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data.Bioinformatics (Oxford, England) · 2024Article
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4 authors.
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Abstract
Dynamic lineage tracing technologies combine genome editing with single-cell sequencing to track cell divisions. We introduce Lineage Analysis via Maximum Likelihood (LAML) to infer a maximum likelihood time-resolved cell lineage tree under the Probabilistic Mixed-type Missing model, which we derive to describe key features of dynamic lineage tracing systems. LAML produces accurate tree topologies with branch lengths representing experimental time between ancestral cells. LAML outperforms existing methods in terms of accuracy and scalability on simulated data, and calculates the timing of cell migrations to metastatic sites in a mouse model of lung adenocarcinoma, revealing distinct epochs of metastasis progression.
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