ArticleNature biotechnology2018
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 363 papers.
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Who cites it
363 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics.Nature biotechnology · 2026Article
- Fibronectin mediates APOE4-driven blood-brain barrier dysfunction in Alzheimer's disease.Nature aging · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- SPACE-seq integrates spatial transcriptomics and lineage tracing in native tissues.Cell stem cell · 2026Article
- Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.Nature methods · 2026Article
- Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease.bioRxiv : the preprint server for biology · 2026Article
- A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations.Science advances · 2026Article
- Brain organoids and genome editing: A new era in understanding human brain development and disorders.Neural regeneration research · 2026Article
- LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage trees.Bioinformatics (Oxford, England) · 2026Article
- Synthetic developmental engineering of human liver organogenesis.Development (Cambridge, England) · 2026Review
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- Accurate trajectory inference in time-series spatial transcriptomics with structurally-constrained optimal transport.Nature communications · 2026Article
- Zebrafish oligodendrocyte lineage cells use the postsynaptic protein Gephyrin to myelinate GABAergic axons and limit myelin sheath growth.Nature communications · 2026Article
- Neuronal microexons modulate arousal via the cAMP-PKA-CREB pathway in zebrafish.Science advances · 2026Article
- Clonal dynamics deviate from neutral drift in zebrafish spermatogenesis.bioRxiv : the preprint server for biology · 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
- A comparison between CARLIN and DNA Typewriter in CRISPR-mediated lineage tracing.BMC bioinformatics · 2026Article
- MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics.Nature communications · 2026Article
303 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ∼60,000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.
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