ArticleMolecular systems biology2020
Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.Bioinformatics (Oxford, England) · 2026Article
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- Chemical genetic interactions elucidate pathways controlling tuberculosis antibiotic efficacy during infection.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Advancements in prospective single-cell lineage barcoding and their applications in research.Genome research · 2024Review
- A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells.Science advances · 2024Article
- A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens.PLoS computational biology · 2024Article
- Article
- Integration of quantitative methods and mathematical approaches for the modeling of cancer cell proliferation dynamics.American journal of physiology. Cell physiology · 2023Review
- CRISPRi screening reveals regulators of tau pathology shared between exosomal and vesicle-free tau.Life science alliance · 2023Article
- DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and immunotherapy response.Nature communications · 2022Article
- Mastering the use of cellular barcoding to explore cancer heterogeneity.Nature reviews. Cancer · 2022Review
- Article
- Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods.Cell systems · 2021Article
- Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast.Microbial cell (Graz, Austria) · 2021Article
- Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in theeLife · 2020Article
- Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics.Molecular systems biology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular DNA barcoding has become a popular approach to study heterogeneity of cell populations and to identify clones with differential response to cellular stimuli. However, there is a lack of reliable methods for statistical inference of differentially responding clones. Here, we used mixtures of DNA-barcoded cell pools to generate a realistic benchmark read count dataset for modelling a range of outcomes of clone-tracing experiments. By accounting for the statistical properties intrinsic to the DNA barcode read count data, we implemented an improved algorithm that results in a significantly lower false-positive rate, compared to current RNA-seq data analysis algorithms, especially when detecting differentially responding clones in experiments with strong selection pressure. Building on the reliable statistical methodology, we illustrate how multidimensional phenotypic profiling enables one to deconvolute phenotypically distinct clonal subpopulations within a cancer cell line. The mixture control dataset and our analysis results provide a foundation for benchmarking and improving algorithms for clone-tracing experiments.
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