ArticlePloS one2012
ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Transposon insertion sequencing of Pseudomonas aeruginosa identifies multiple intersecting pathways essential for extreme colistin resistance.PLoS pathogens · 2026Article
- Comparative analysis of gene importance inmSystems · 2026Article
- Introducing gold-standard essential gene datasets for Pseudomonas aeruginosa to enhance Tn-Seq analyses.PLoS computational biology · 2026Article
- Article
- High-Throughput Tn-Seq Screens Identify Both Known and Novel Pseudomonas putida KT2440 Genes Involved in Metal Tolerance.Environmental microbiology · 2025Article
- Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.Frontiers in immunology · 2025Review
- Essential Genes Discovery in Microorganisms by Transposon-Directed Sequencing (Tn-Seq): Experimental Approaches, Major Goals, and Future Perspectives.International journal of molecular sciences · 2024Review
- A deoxyviolacein-based transposon insertion vector for pigmented tracer studies.MicrobiologyOpen · 2024Article
- Article
- Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight.BMC genomics · 2023Article
- Elucidation of Essential Genes and Mutant Fitness during Adaptation toward Nitrogen Fixation Conditions in the Endophyte Azoarcus olearius BH72 Revealed by Tn-Seq.Microbiology spectrum · 2022Article
- Gluconacetobacter diazotrophicus Gene Fitness during Diazotrophic Growth.Applied and environmental microbiology · 2022Article
- Development of mass allelic exchange, a technique to enable sexual genetics inProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride.Environmental microbiology · 2022Article
- Genomic landscapes of bacterial transposons and their applications in strain improvement.Applied microbiology and biotechnology · 2022Review
- In silico Methods for Identification of Potential Therapeutic Targets.Interdisciplinary sciences, computational life sciences · 2022Review
- Gradients in gene essentiality reshape antibacterial research.FEMS microbiology reviews · 2022Review
- Model-based identification of conditionally-essential genes from transposon-insertion sequencing data.PLoS computational biology · 2022Article
- Aminoglycoside-resistance gene signatures are predictive of aminoglycoside MICs for carbapenem-resistant Klebsiella pneumoniae.The Journal of antimicrobial chemotherapy · 2022Article
- The Use of Tn-Seq and the FiTnEss Analysis to Define the Core Essential Genome of Pseudomonas aeruginosa.Methods in molecular biology (Clifton, N.J.) · 2022Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.
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