ArticleMethods in molecular biology (Clifton, N.J.)2022
Analysis of Gene Essentiality from TnSeq Data Using Transit.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- MetF-Dependent Methionine Biosynthesis Is Required for Mycobacterium tuberculosis Survival and In Vivo Persistence.MicrobiologyOpen · 2026Article
- ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.PLoS computational biology · 2026Article
- Introducing gold-standard essential gene datasets for Pseudomonas aeruginosa to enhance Tn-Seq analyses.PLoS computational biology · 2026Article
- Analysis of essential genes inJournal of bacteriology · 2025Article
- Genome-wide phenotypic insights into mycobacterial virulence using Drosophila melanogaster.PLoS pathogens · 2025Article
- The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin.Scientific reports · 2025Article
- Analysis of Essential Genes inbioRxiv : the preprint server for biology · 2025Article
- TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity.NPJ vaccines · 2025Article
- Genome-wide mutagenesis identifies factors involved in MRSA vaginal colonization.Cell reports · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Pangenome evaluation of gene essentiality inMicrobiology spectrum · 2024Article
- Fluoride-related changes in the fetal cord blood proteome; a pilot study.Environmental health : a global access science source · 2024Article
- Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight.BMC genomics · 2023Article
- Article
- Comprehensive essentiality analysis of themBio · 2023Article
- A mutant fitness assay identifies bacterial interactions in a model ocean hot spot.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- pBLAM1-x: standardized transposon tools for high-throughput screening.Synthetic biology (Oxford, England) · 2023Article
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1 author at 1 institution in 1 country.
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Abstract
TnSeq, or sequencing of transposon insertion libraries, has proven to be a valuable method for probing the functions of genes in a wide range of bacteria. TnSeq has found many applications for studying genes involved in core functions (such as cell division or metabolism), stress response, virulence, etc., as well as to identify potential drug targets. Two of the most commonly used transposons in practice are Himar1, which inserts randomly at TA dinucleotides, and Tn5, which can insert more broadly throughout the genome. These insertions cause putative gene function disruption, and clones with insertions in genes that cannot tolerate disruption (in a given condition) are eliminated from the population. Deep sequencing can be used to efficiently profile the surviving members, with insertions in genes that can be inferred to be non-essential. Data from TnSeq experiments (i.e. transposon insertion counts at specific genomic locations) is inherently noisy, making rigorous statistical analysis (e.g. quantifying significance) challenging. In this chapter, we describe Transit, a Python-based software package for analyzing TnSeq data that combines a variety of data processing tools, quality assessment methods, and analytical algorithms for identifying essential (or conditionally essential) genes.
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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.