ArticleCell genomics2024
Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.
Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Single-Cell RNA-Seq Reveals Chromosomal Instability-Associated Transcriptomic Profiles in Breast Cancer.Biomedicines · 2026Article
- Hierarchical lineage tracing reveals diverse pathways of cytarabine resistance.Nature communications · 2026Article
- Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases.Nature methods · 2026Article
- Derivation of oligonucleotide barcodes that are absent from natural sequences.Bioinformatics advances · 2026Article
- Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems.Cell systems · 2025Review
- Droplet-based single-cell RNA sequencing: decoding cellular heterogeneity for breakthroughs in cancer, reproduction, and beyond.Journal of translational medicine · 2025Review
- Dysregulated RNA splicing impairs regeneration in alcohol-associated liver disease.Nature communications · 2025Article
- Fluctuation structure predicts genome-wide perturbation outcomes.Research square · 2025Article
- Resolving the design principles that control post-natal vascular growth and scaling.Cell systems · 2025Article
- Fluctuation structure predicts genome-wide perturbation outcomes.bioRxiv : the preprint server for biology · 2025Article
- Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.ACS synthetic biology · 2025Article
- Mapping cell-cell fusion at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- Improving doublet cell removal efficiency through multiple algorithm runs.Computational and structural biotechnology journal · 2025Article
- Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells.Genome biology · 2024Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.
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