ReviewJournal of molecular evolution2023
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.
Review in Journal of molecular evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Comparative phylogenetic analysis of breast cancer susceptibility genes reveals evolutionary conservation supporting diagnostic barcode design.Annals of medicine and surgery (2012) · 2026Article
- Hierarchical lineage tracing reveals diverse pathways of cytarabine resistance.Nature communications · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Determinants of metal import and specificity in a bacterial transporter.bioRxiv : the preprint server for biology · 2026Article
- Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations.PLoS computational biology · 2026Article
- Genotyping by sequencing reveals a chromosome A04 QTL governing whitefly resistance in upland cotton.Scientific reports · 2025Article
- An empirical long-term competition among natural yeast isolates reveals that short-term fitness largely but not entirely predicts long-term outcomes.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive profiling of activity and specificity of RNA-guided transposons reveals opportunities to engineer improved variants.Nucleic acids research · 2025Article
- Quantifying DNA point mutations in commercially available AAV reporter vectors and plasmids.Molecular therapy. Methods & clinical development · 2025Article
- Highly replicated experiments studying complex genotypes using nested DNA barcodes.G3 (Bethesda, Md.) · 2025Article
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- Identifying optimal conditions for precise knock-in of exogenous DNA into the zebrafish genome.Development (Cambridge, England) · 2025Article
- Hierarchical Lineage Tracing Reveals Diverse Pathways of AML Treatment Resistance.bioRxiv : the preprint server for biology · 2025Article
- Digital sequencing is improved by using structured unique molecular identifiers.Genome biology · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Improving the Accuracy of Bulk Fitness Assays by Correcting Barcode Processing Biases.Molecular biology and evolution · 2024Article
- Flexible parsing, interpretation, and editing of technical sequences with splitcode.Bioinformatics (Oxford, England) · 2024Article
- Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.Cell reports methods · 2024Article
- ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.Nucleic acids research · 2024Article
- Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.Nature microbiology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.
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Registered trials
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.