ArticleBioinformatics (Oxford, England)2013
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 89 citations in OpenAlex.
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- Analysis of Essential Genes inbioRxiv : the preprint server for biology · 2025Article
- Saturated Transposon Analysis in Yeast as a one-step method to quantify the fitness effects of gene disruptions on a genome-wide scale.PloS one · 2025Article
- Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome.mLife · 2024Article
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- Whole genome-scale assessment of gene fitness of Novosphingobium aromaticavorans during spaceflight.BMC genomics · 2023Article
- Bile acid fitness determinants of abioRxiv : the preprint server for biology · 2023Article
- Functional Whole Genome Screen of Nutrient-StarvedMicroorganisms · 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
- Article
- Model-based identification of conditionally-essential genes from transposon-insertion sequencing data.PLoS computational biology · 2022Article
- Identification of putative essential protein domains from high-density transposon insertion sequencing.Scientific reports · 2022Article
- A large-scale whole-genome sequencing analysis reveals false positives of bacterial essential genes.Applied microbiology and biotechnology · 2022Article
- Analysis of Gene Essentiality from TnSeq Data Using Transit.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME.NPJ systems biology and applications · 2021Article
- Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets.mSystems · 2021Article
- 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme.Communications biology · 2021Article
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Authors and funding
6 authors at 2 institutions in 1 country.
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Abstract
motivationNext-generation sequencing affords an efficient analysis of transposon insertion libraries, which can be used to identify essential genes in bacteria. To analyse this high-resolution data, we present a formal Bayesian framework for estimating the posterior probability of essentiality for each gene, using the extreme-value distribution to characterize the statistical significance of the longest region lacking insertions within a gene. We describe a sampling procedure based on the Metropolis-Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters.
resultsUsing a sequence dataset from a transposon library for Mycobacterium tuberculosis, we show that this Bayesian approach predicts essential genes that correspond well with genes shown to be essential in previous studies. Furthermore, we show that by using the extreme-value distribution to characterize genomic regions lacking transposon insertions, this method is capable of identifying essential domains within genes. This approach can be used for analysing transposon libraries in other organisms and augmenting essentiality predictions with statistical confidence scores.
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