ArticleProceedings of the National Academy of Sciences of the United States of America2020
Lineage reconstruction from clonal correlations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.Bioinformatics (Oxford, England) · 2026Article
- Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Trajectory inference for a branching SDE model of cell differentiation via lineage tracing.Journal of mathematical biology · 2026Article
- Article
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice.Nature immunology · 2025Article
- Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate.bioRxiv : the preprint server for biology · 2025Article
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases.bioRxiv : the preprint server for biology · 2025Article
- Advancements in prospective single-cell lineage barcoding and their applications in research.Genome research · 2024Review
- Mapping lineage-traced cells across time points with moslin.Genome biology · 2024Article
- Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision.Immunity · 2024Article
- Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes.NAR genomics and bioinformatics · 2023Article
- ClonoCluster: A method for using clonal origin to inform transcriptome clustering.Cell genomics · 2023Article
- Article
- Connecting past and present: single-cell lineage tracing.Protein & cell · 2022Review
- Recent Advances in Monitoring Stem Cell Status and Differentiation Using Nano-Biosensing Technologies.Nanomaterials (Basel, Switzerland) · 2022Review
- Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees.PLoS computational biology · 2022Article
- A New Generation of Lineage Tracing Dynamically Records Cell Fate Choices.International journal of molecular sciences · 2022Review
- Cell types as species: Exploring a metaphor.Frontiers in plant science · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A central task in developmental biology is to learn the sequence of fate decisions that leads to each mature cell type in a tissue or organism. Recently, clonal labeling of cells using DNA barcodes has emerged as a powerful approach for identifying cells that share a common ancestry of fate decisions. Here we explore the idea that stochasticity of cell fate choice during tissue development could be harnessed to read out lineage relationships after a single step of clonal barcoding. By considering a generalized multitype branching process, we determine the conditions under which the final distribution of barcodes over observed cell types encodes their bona fide lineage relationships. We then propose a method for inferring the order of fate decisions. Our theory predicts a set of symmetries of barcode covariance that serves as a consistency check for the validity of the method. We show that broken symmetries may be used to detect multiple paths of differentiation to the same cell types. We provide computational tools for general use. When applied to barcoding data in hematopoiesis, these tools reconstruct the classical hematopoietic hierarchy and detect couplings between monocytes and dendritic cells and between erythrocytes and basophils that suggest multiple pathways of differentiation for these lineages.
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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.