ArticleNucleic acids research2019
Cell lineage inference from SNP and scRNA-Seq data.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Late-stage dedifferentiation and epigenetic memory of cancer stem cells in hepatocellular carcinoma.Journal of translational medicine · 2026Article
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
- Tracking Somatic Mutations for Lineage Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Bayesian Phylogenetic Lineage Reconstruction with Loss of Heterozygosity Mutations Derived from Single-Cell RNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning.Nature communications · 2024Article
- Critical transition and reversion of tumorigenesis.Experimental & molecular medicine · 2023Review
- Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.Communications biology · 2022Article
- Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development.Cell systems · 2022Article
- Redefining intestinal immunity with single-cell transcriptomics.Mucosal immunology · 2022Review
- LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures.DNA repair · 2021Review
- Article
- Single-cell RNA sequencing in vision research: Insights into human retinal health and disease.Progress in retinal and eye research · 2021Review
- The Role of Cell Tracing and Fate Mapping Experiments in Cardiac Outflow Tract Development, New Opportunities through Emerging Technologies.Journal of cardiovascular development and disease · 2021Review
- Heterogeneity of cell composition and origin identified by single-cell transcriptomics in renal cysts of patients with autosomal dominant polycystic kidney disease.Theranostics · 2021Article
- Exploring Additional Valuable Information From Single-Cell RNA-Seq Data.Frontiers in cell and developmental biology · 2020Review
- Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data.Genome biology · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Several recent studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. Recently, CRISPR has also been used to reconstruct lineage trees by inserting random mutations. However, both approaches suffer from drawbacks that limit their use. Here, we develop a method to detect significant, cell type specific, sequence mutations from scRNA-Seq data. We show that only a few mutations are enough for reconstructing good branching models. Integrating these mutations with expression data further improves the accuracy of the reconstructed models. As we show, the majority of mutations we identify are likely RNA editing events indicating that such information can be used to distinguish cell types.
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Registered trials
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