ArticleNature communications2023
LinRace: cell division history reconstruction of single cells using paired lineage barcode and gene expression data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Article
- Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis.Nature genetics · 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
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML.Genome biology · 2025Article
- Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.Nature communications · 2025Article
- Advancements in prospective single-cell lineage barcoding and their applications in research.Genome research · 2024Review
- Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data.Cell genomics · 2024Article
- Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data.Bioinformatics (Oxford, England) · 2024Article
- Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.Cell reports methods · 2024Article
- Studying temporal dynamics of single cells: expression, lineage and regulatory networks.Biophysical reviews · 2024Review
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4 authors.
Funding
Abstract
Lineage tracing technology using CRISPR/Cas9 genome editing has enabled simultaneous readouts of gene expressions and lineage barcodes in single cells, which allows for inference of cell lineage and cell types at the whole organism level. While most state-of-the-art methods for lineage reconstruction utilize only the lineage barcode data, methods that incorporate gene expressions are emerging. Effectively incorporating the gene expression data requires a reasonable model of how gene expression data changes along generations of divisions. Here, we present LinRace (Lineage Reconstruction with asymmetric cell division model), which integrates lineage barcode and gene expression data using asymmetric cell division model and infers cell lineages and ancestral cell states using Neighbor-Joining and maximum-likelihood heuristics. On both simulated and real data, LinRace outputs more accurate cell division trees than existing methods. With inferred ancestral states, LinRace can also show how a progenitor cell generates a large population of cells with various functionalities.
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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.