ArticleMolecular cell2022
Machine-learning-optimized Cas12a barcoding enables the recovery of single-cell lineages and transcriptional profiles.
Article in Molecular cell, 2022. 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.
- PROFET predicts continuous gene expression dynamics from scRNA-seq data to elucidate heterogeneity of cancer treatment responses.Cell systems · 2026Article
- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Efficient and multiplexed somatic genome editing with Cas12a mice.Nature biomedical engineering · 2025Article
- Molecular circuits for genomic recording of cellular events.Trends in genetics : TIG · 2025Review
- Stereotyped Subclones Revealed by High-Density Single-Cell Lineage Tracing Support Robust Development.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Advances in CRISPR-Cas9 in lineage tracing of model animals.Animal models and experimental medicine · 2025Review
- Loss of YTHDC1 mExperimental & molecular medicine · 2025Article
- Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.Nature communications · 2025Article
- Mapping lineage-traced cells across time points with moslin.Genome biology · 2024Article
- Computationally guided high-throughput engineering of an anti-CRISPR protein for precise genome editing in human cells.Cell reports methods · 2024Article
- Clonal tracking in cancer and metastasis.Cancer metastasis reviews · 2024Review
- PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes.Nature biotechnology · 2024Article
- High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo.Cold Spring Harbor perspectives in medicine · 2023Review
- Dissecting metastasis using preclinical models and methods.Nature reviews. Cancer · 2023Review
- Small Molecules for Enhancing the Precision and Safety of Genome Editing.Molecules (Basel, Switzerland) · 2022Review
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Authors and funding
12 authors.
Funding
Abstract
The development of CRISPR-based barcoding methods creates an exciting opportunity to understand cellular phylogenies. We present a compact, tunable, high-capacity Cas12a barcoding system called dual acting inverted site array (DAISY). We combined high-throughput screening and machine learning to predict and optimize the 60-bp DAISY barcode sequences. After optimization, top-performing barcodes had ∼10-fold increased capacity relative to the best random-screened designs and performed reliably across diverse cell types. DAISY barcode arrays generated ∼12 bits of entropy and ∼66,000 unique barcodes. Thus, DAISY barcodes-at a fraction of the size of Cas9 barcodes-achieved high-capacity barcoding. We coupled DAISY barcoding with single-cell RNA-seq to recover lineages and gene expression profiles from ∼47,000 human melanoma cells. A single DAISY barcode recovered up to ∼700 lineages from one parental cell. This analysis revealed heritable single-cell gene expression and potential epigenetic modulation of memory gene transcription. Overall, Cas12a DAISY barcoding is an efficient tool for investigating cell-state dynamics.
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