ArticleBioinformatics (Oxford, England)2024
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- WISH-barcoding of Salmonella Typhimurium ATCC14028s strains for population dynamics studies in vivo.PloS one · 2026Article
- Salmonella multimutants enable efficient identification of SPI-2 effector protein function in gut inflammation and systemic colonization.Nature communications · 2025Article
- DNA-Barcoding for Cultivar Identification and Intraspecific Diversity Analysis of Agricultural Crops.International journal of molecular sciences · 2025Review
- Strain-specific galactose utilization by commensal E. coli mitigates Salmonella establishment in the gut.PLoS pathogens · 2025Article
- Interplay between chemotaxis, quorum sensing, and metabolism regulates Escherichia coli-Salmonella Typhimurium interactions in vivo.PLoS pathogens · 2025Article
- Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner.Nature communications · 2025Article
- Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.Nature microbiology · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
motivationDNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills.
resultsHere, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery. AVAILABILITY AND IMPLEMENTATION: The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app.
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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.