ArticleBMC bioinformatics2017
TnseqDiff: identification of conditionally essential genes in transposon sequencing studies.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Introducing gold-standard essential gene datasets for Pseudomonas aeruginosa to enhance Tn-Seq analyses.PLoS computational biology · 2026Article
- Reviewing the complexities of bacterial biocide susceptibility and in vitro biocide adaptation methodologies.npj antimicrobials and resistance · 2025Review
- Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.Nature communications · 2025Article
- Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.Frontiers in immunology · 2025Review
- Transposon sequencing reveals metabolic pathways essential for Mycobacterium tuberculosis infection.PLoS pathogens · 2024Article
- Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight.BMC genomics · 2023Article
- Klebsiella pneumoniae causes bacteremia using factors that mediate tissue-specific fitness and resistance to oxidative stress.PLoS pathogens · 2023Article
- Mycobacterium tuberculosis Requires the Outer Membrane Lipid Phthiocerol Dimycocerosate for Starvation-Induced Antibiotic Tolerance.mSystems · 2023Article
- Article
- Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp.Applied and environmental microbiology · 2022Article
- The ADP-Heptose Biosynthesis Enzyme GmhB is a Conserved Gram-Negative Bacteremia Fitness Factor.Infection and immunity · 2022Article
- Gradients in gene essentiality reshape antibacterial research.FEMS microbiology reviews · 2022Review
- Analysis of Gene Essentiality from TnSeq Data Using Transit.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A Genome-Scale Antibiotic Screen in Serratia marcescens Identifies YdgH as a Conserved Modifier of Cephalosporin and Detergent Susceptibility.Antimicrobial agents and chemotherapy · 2021Article
- Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses.BMC microbiology · 2021Article
- Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing.Journal of bacteriology · 2021Article
- Genetic Approaches to Uncover Gene Products Involved in Iron-Sulfur Protein Maturation: High-Throughput Genomic Screening Using Transposon Sequencing.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Transposon Insertion Sequencing, a Global Measure of Gene Function.Annual review of genetics · 2020Review
- Escherichia coli CFT073 Fitness Factors during Urinary Tract Infection: Identification Using an Ordered Transposon Library.Applied and environmental microbiology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundTn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that multiple mutants in a gene provides independent evidence to prioritize that gene as being essential. The existing methods do not account for this feature or rely on a high-density transposon library. Moreover, these methods are unable to accommodate complex designs.
resultsThe method proposed here is specifically designed for the analysis of Tn-Seq data. It utilizes two steps to estimate the conditional essentiality for each gene in the genome. First, it collects evidence of conditional essentiality for each insertion by comparing read counts of that insertion between conditions. Second, it combines insertion-level evidence for the corresponding gene. It deals with data from both low- and high-density transposon libraries and accommodates complex designs. Moreover, it is very fast to implement. The performance of the proposed method was tested on simulated data and experimental Tn-Seq data from Serratia marcescens transposon mutant library used to identify genes that contribute to fitness in a murine model of infection.
conclusionWe describe a new, efficient method for identifying conditionally essential genes in Tn-Seq experiments with high detection sensitivity and specificity. It is implemented as TnseqDiff function in R package Tnseq and can be installed from the Comprehensive R Archive Network, CRAN.
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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.